Automation Engineer Jobs in Washington
Automation Engineer jobs in Washington are in high demand, concentrated in aerospace and defense manufacturing, semiconductor fabrication, and advanced logistics, with openings at every level from entry-level controls technician to senior systems engineer. Seattle, Redmond, and the Tri-Cities corridor around Richland anchor most hiring activity, where employers such as Boeing, Microsoft, and Hanford contractor systems teams maintain large, established automation engineering functions. The most sought-after specialties in Washington include PLC and SCADA programming, robotics integration, and process automation for clean-room and regulated-manufacturing environments. Find a role that fits below and apply directly.
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Senior Automation Engineer– Molecular Tool Development
The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.
The mission of Scientific Shared Resources and Technologies is to enable biological insight through technology innovation, development and application in partnership with the Accelerators at the Allen Institute. This includes generation of world leading datasets.
We are searching for an Automation Engineer, Senior to lead the automation group in the Molecular Tool Development team within Shared Resources. The mission of the Molecular Tool Development team is to pioneer, develop, and deploy advanced molecular tools and cutting-edge liquid handling automation across the Allen Institute. By serving as a centralized engine of innovation, the team partners directly with accelerators and high-throughput standardized services to seamlessly translate novel workflows into robust, scalable pipelines. This role sets the team’s automation strategy and partners with scientists and technical teams across the Allen Institute to translate emerging molecular methods and complex laboratory workflows into reliable, scalable automation solutions. The Automation Engineer, Senior leads automation initiatives through requirements definition, design, integration, validation, deployment, and ongoing improvement; establishes team technical standards and best practices; and guides the adoption of automation across diverse scientific programs. The position also manages and develops the automation group in the Molecular Tool Development team, aligns staff and financial resources with Institute priorities, and ensures the team delivers reproducible, high-throughput workflows that expand scientific capabilities across the Institute.
At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly.
We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.
We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.
Essential Functions
- Partner with scientists and technical stakeholders early in project lifecycles to identify automation opportunities, define technical requirements, translate scientific concepts into scalable engineering plans, and develop automation roadmaps that accelerate scientific and operational outcomes.
- Build, lead and manage the automation group in the Molecular Tool Development team, including recruiting, coaching, performance management, resource allocation, and workforce planning to meet Institute-wide automation needs. This includes tracking financial spend and cost recovery models
- Develop and maintain strategic vendor partnerships and provide technical leadership for equipment evaluation, procurement, implementation, and ongoing support
- Drive the full lifecycle of automation development including requirements gathering, custom scripting, system validation, release, and ongoing operational support
- Design and integrate automation platforms across complex workflows, including lab-in-the-loop systems, proteomics, functional cell assays, and NGS assays enabling scalable, high-throughput research and scientific discovery
- Demonstrate impact through increased scientific discovery, presentations and publications
- Establish Institute-wide technical standards, scripting guidelines, and validation protocols to ensure high-throughput platform reliability, reproducibility, and operational excellence across scientific programs
- Evaluate emerging automation technologies and approaches and recommend adoption strategies that advance scientific capabilities, scalability, and operational effectiveness across the Institute
- Lead cross-functional collaboration with staff scientists, computational biologists, engineers, and operational teams to align automation solutions with scientific priorities and Institute objectives
- Develop training materials, provide instruction on validated workflows, and foster team growth through mentoring, hiring, employee development, and performance management processes
Required Education and Experience
- Bachelor’s degree in life sciences, engineering or biotech related field (or combination of degree and experience) and 5 years of relevant experience
- 5 years of experience in laboratory automation, liquid handling, and high-throughput molecular assay development, with demonstrated progression into technical roles
- Deep expertise in method development for liquid handling robots (e.g. Tecan, Hamilton, Integra, etc.) and associated scripting software
- Demonstrated proficiency translating complex manual workflows into scalable, validated automated liquid handling solutions
- Experience with LIMS integration and barcode-based sample tracking in high-throughput environments
Preferred Education and Experience
- Bachelor’s degree in life sciences, engineering or biotech related field (or combination of degree and experience) and 5 -7 years of relevant experience
- Proven ability to lead cross-functional projects with significant organizational impact, managing complex dependencies and delivering results with minimal supervision
- Experience authoring verification protocols, SOPs, and validation documentation to industry or regulatory standards
- Excellent communication and stakeholder management skills, with demonstrated ability to influence technical direction across teams
- Experience with NGS library preparation workflows and automating these protocols, at scale
- Background in functional cell assays
- Publication record or technical contributions to open-access datasets or scientific resources
- Working knowledge of scripting or data analysis tools (e.g., R, Python) for QC and pipeline reporting
Physical Demands
- Occasional lifting to 30 pounds
- Fine motor movements in fingers/hands to operate computers and other office equipment
- Working at a computer and using a mouse for extended periods of time
Expected Hours of Work
- Occasional evening and weekend hours required
- This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.
Additional Comments
- **Please note, this opportunity does sponsor work visas
- **Please note, this opportunity does offer relocation assistance
Annualized Salary Range
- $137,050 - $171,250*
- Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.
Benefits
- Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.
It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities
Senior Automation Engineer– Molecular Tool Development
The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.
The mission of Scientific Shared Resources and Technologies is to enable biological insight through technology innovation, development and application in partnership with the Accelerators at the Allen Institute. This includes generation of world leading datasets.
We are searching for an Automation Engineer, Senior to lead the automation group in the Molecular Tool Development team within Shared Resources. The mission of the Molecular Tool Development team is to pioneer, develop, and deploy advanced molecular tools and cutting-edge liquid handling automation across the Allen Institute. By serving as a centralized engine of innovation, the team partners directly with accelerators and high-throughput standardized services to seamlessly translate novel workflows into robust, scalable pipelines. This role sets the team’s automation strategy and partners with scientists and technical teams across the Allen Institute to translate emerging molecular methods and complex laboratory workflows into reliable, scalable automation solutions. The Automation Engineer, Senior leads automation initiatives through requirements definition, design, integration, validation, deployment, and ongoing improvement; establishes team technical standards and best practices; and guides the adoption of automation across diverse scientific programs. The position also manages and develops the automation group in the Molecular Tool Development team, aligns staff and financial resources with Institute priorities, and ensures the team delivers reproducible, high-throughput workflows that expand scientific capabilities across the Institute.
At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly.
We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.
We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.
Essential Functions
- Partner with scientists and technical stakeholders early in project lifecycles to identify automation opportunities, define technical requirements, translate scientific concepts into scalable engineering plans, and develop automation roadmaps that accelerate scientific and operational outcomes.
- Build, lead and manage the automation group in the Molecular Tool Development team, including recruiting, coaching, performance management, resource allocation, and workforce planning to meet Institute-wide automation needs. This includes tracking financial spend and cost recovery models
- Develop and maintain strategic vendor partnerships and provide technical leadership for equipment evaluation, procurement, implementation, and ongoing support
- Drive the full lifecycle of automation development including requirements gathering, custom scripting, system validation, release, and ongoing operational support
- Design and integrate automation platforms across complex workflows, including lab-in-the-loop systems, proteomics, functional cell assays, and NGS assays enabling scalable, high-throughput research and scientific discovery
- Demonstrate impact through increased scientific discovery, presentations and publications
- Establish Institute-wide technical standards, scripting guidelines, and validation protocols to ensure high-throughput platform reliability, reproducibility, and operational excellence across scientific programs
- Evaluate emerging automation technologies and approaches and recommend adoption strategies that advance scientific capabilities, scalability, and operational effectiveness across the Institute
- Lead cross-functional collaboration with staff scientists, computational biologists, engineers, and operational teams to align automation solutions with scientific priorities and Institute objectives
- Develop training materials, provide instruction on validated workflows, and foster team growth through mentoring, hiring, employee development, and performance management processes
Required Education and Experience
- Bachelor’s degree in life sciences, engineering or biotech related field (or combination of degree and experience) and 5 years of relevant experience
- 5 years of experience in laboratory automation, liquid handling, and high-throughput molecular assay development, with demonstrated progression into technical roles
- Deep expertise in method development for liquid handling robots (e.g. Tecan, Hamilton, Integra, etc.) and associated scripting software
- Demonstrated proficiency translating complex manual workflows into scalable, validated automated liquid handling solutions
- Experience with LIMS integration and barcode-based sample tracking in high-throughput environments
Preferred Education and Experience
- Bachelor’s degree in life sciences, engineering or biotech related field (or combination of degree and experience) and 5 -7 years of relevant experience
- Proven ability to lead cross-functional projects with significant organizational impact, managing complex dependencies and delivering results with minimal supervision
- Experience authoring verification protocols, SOPs, and validation documentation to industry or regulatory standards
- Excellent communication and stakeholder management skills, with demonstrated ability to influence technical direction across teams
- Experience with NGS library preparation workflows and automating these protocols, at scale
- Background in functional cell assays
- Publication record or technical contributions to open-access datasets or scientific resources
- Working knowledge of scripting or data analysis tools (e.g., R, Python) for QC and pipeline reporting
Physical Demands
- Occasional lifting to 30 pounds
- Fine motor movements in fingers/hands to operate computers and other office equipment
- Working at a computer and using a mouse for extended periods of time
Expected Hours of Work
- Occasional evening and weekend hours required
- This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.
Additional Comments
- **Please note, this opportunity does sponsor work visas
- **Please note, this opportunity does offer relocation assistance
Annualized Salary Range
- $137,050 - $171,250*
- Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.
Benefits
- Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.
It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities
See All 81 Automation Engineer Jobs in Washington
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Find Automation Engineer JobsAutomation Engineer Jobs by City in Washington
Where Washington roles are concentrated, by current openings.
Automation Engineer Job Market in Washington
A snapshot from current Washington openings, updated as new roles post.
Who's Hiring
- Amazon22
- Blue Origin8
- Sargent & Lundy4
- GEICO3
- Janicki Industries3
Top Industries Hiring
- Technology & Software
- Retail
- E-Commerce & Online Marketplaces
- Manufacturing
- Aerospace & Defense
What Washington Employers Look For
The qualifications that appear most often in automation engineer jobs across Washington.
- Bachelor's degree in electrical engineering, mechanical engineering, or a closely related field
- Hands-on experience with PLC programming platforms such as Allen-Bradley or Siemens
- Proficiency with SCADA systems and industrial communication protocols such as Modbus or EtherNet/IP
- Demonstrated ability to design, test, and commission automated production or process control systems
- Familiarity with robotics integration and motion control in manufacturing or clean-room environments
- Strong documentation skills including functional design specs, P&IDs, and validation protocols
Automation Engineer Jobs in Washington: Frequently Asked Questions
How do you become a automation engineer in Washington?
Automation engineers in Washington typically enter the field with a bachelor's degree in electrical, mechanical, or systems engineering from a state institution such as the University of Washington or Washington State University. No state-issued license is required to hold the title, though engineers who sign off on public-works or safety-critical systems must obtain a Professional Engineer license through the Washington State Board of Registration for Professional Engineers and Land Surveyors. Employers in aerospace and semiconductor manufacturing strongly prefer candidates with hands-on PLC and controls experience gained through co-ops, internships, or technical certificate programs.
How much do automation engineers make in Washington?
Automation engineers in Washington earn a median of about $134,570 a year, based on May 2025 Bureau of Labor Statistics wage data, ranging from around $81,280 for the lowest 10% to over $196,120 for the top 10%. Pay rises with experience, specialty, and employer.
Which companies hire automation engineers in Washington?
Employers hiring automation engineers in Washington right now include Amazon, Blue Origin, and Sargent & Lundy, based on current listings on Migrate Mate as of September 2026. Washington's dense concentration of aerospace manufacturers, semiconductor fabs, and large-scale logistics operations means consistent demand across both the Puget Sound region and the inland industrial corridor near the Tri-Cities.
Which Washington cities have the most automation engineer jobs?
Seattle, Redmond, and Bellevue lead Washington for automation engineer openings. Seattle and Redmond drive demand through aerospace primes, cloud-infrastructure campuses, and advanced manufacturing facilities, while the Tri-Cities area around Richland sustains a distinct cluster of process-automation roles tied to energy and government-contract industrial operations at and around the Hanford site.
Are there remote automation engineer jobs in Washington?
Yes, but they're rare. Automation engineering is fundamentally a hands-on discipline: commissioning equipment, troubleshooting live systems, and validating production lines all require physical presence. About 59% of automation engineer openings tied to Washington are remote or hybrid as of September 2026, and those positions tend to concentrate in software-heavy sub-disciplines such as SCADA configuration, simulation modeling, and controls system architecture where bench work can be deferred.
How can I get hired as a automation engineer in Washington with little or no experience?
The most realistic entry path is an engineering technician or controls technician role at a Washington manufacturer, which typically requires only an associate degree or technical certificate and provides direct exposure to PLCs and automated systems. Boeing and its Puget Sound supplier network regularly hire entry-level manufacturing engineers and process technicians through campus recruiting at institutions such as Bellingham Technical College and South Puget Sound Community College. Building a portfolio of personal PLC ladder-logic projects and earning a vendor certification from Rockwell Automation or Siemens significantly strengthens a candidate's application before they have professional site experience.
Where can I find and apply to automation engineer jobs in Washington?
You can find and apply to automation engineer jobs in Washington on Migrate Mate, which lists current Washington openings across Seattle, Redmond, the Tri-Cities, and surrounding areas. Find the roles that fit your background and apply directly from each listing.
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