Application Engineer Jobs in New York
Application Engineer jobs in New York are in strong and consistent demand, concentrated in industrial automation, enterprise software, semiconductors, and advanced manufacturing, with openings at every level from entry-level associate through senior and principal roles. The heaviest hiring is in New York City, Long Island, and the Hudson Valley corridor, where established employers like IBM, Siemens, and Zebra Technologies maintain deep engineering operations. The most sought-after specializations include PLC and SCADA systems, SaaS integration, and embedded hardware applications. Find a role that fits below and apply directly.
Find Application Engineer JobsOverview
Showing 5 of 68+ Application Engineer jobs











Work Schedule
Standard (Mon-Fri)
Environmental Conditions
Able to lift 40 lbs. without assistance, Adherence to all Good Manufacturing Practices (GMP) Safety Standards, Cold Room/Freezers -22 degrees F/-6 degrees C, Laboratory Setting, Office, Some degree of PPE (Personal Protective Equipment) required (safety glasses, gowning, gloves, lab coat, ear plugs etc.)
Job Description
When you’re part of the team at Thermo Fisher Scientific, you’ll do meaningful work, that makes a positive impact on a global scale. Join 100,000 colleagues who bring our Mission to life each day to enable our customers to make the world healthier, cleaner and safer. You’ll find the resources here to achieve your career goals and help take science a step beyond by developing solutions for some of the world’s toughest challenges, like protecting the environment, making sure our food is safe or helping find cures for cancer.
Division
You will be a part of the Global Team of Field Application Scientists within the Materials and Structural Analysis Division (MSD) of Thermo Fisher Scientific.
Location: Onsite New York City, NY
How will you make an impact?
Our Team has one, unified goal – to help our customers be successful in their research. We do this primarily by delivering world-class training and support for our customers with cryo-electron microscopy. In addition, we also support our field service, marketing, sales, and R&D teams.
What will you do?
Microscope management of service issues within the scope of a regular end user’s responsibility, including but not limited to the following:
- Coordinate with site lab personnel and with Supplier’s service team to schedule service. Checking on data quality/alignments when needed, ensuring the facility is stocked with various microscopy needs.
- Proactively designing and implementing improvements in the workflow to improve speed, quality and reliability of data collection on Supplier’s equipment.
- Maintaining open communication with site scientific team to enable IT requirements for Supplier instrument operation.
- Work closely with users for microscope time slot scheduling and management.
- Collaborate with site Scientists to ensure all reasonable documentation regarding the scope of work is completed in a timely manner.
- The scientist will follow Supplier’s standard operating procedure for reporting service issues and will open service calls as necessary (at which point the issue will be owned and managed by Supplier’s field service team who will interface with both the scientist and site). Microscope maintenance is outside of the scope of this Project Agreement and shall be the subject of one or more separate agreements.
- Grid loading and data collection.
- If time permits, grid preparation and data processing.
- Receiving of Cryo-EM samples and storing them properly.
- New features and methods testing.
- Training of users regarding grid preparation and data collection.
- Co-author publications as approved in writing by site and Supplier.
- Adhere to confidentiality or NDA agreements.
- Ability to work remotely on projects solely if deemed necessary by the site due to circumstances outside of normal control (e.g., restrictions on in-person lab work due to COVID).
How will you get here?
Minimum Experience & Education
- 3+ years’ experience in routine equipment maintenance, microscope operation, and computational aspects of Cryo-EM.
- 1+ years’ experience leading efforts to maintain and elevate the Cryo-EM customer experience.
- Strong track record of scientific accomplishments within one or more Cryo-EM techniques.
- Ph.D. degree with a focus on Cryo-EM structural biology.
Knowledge, Skills, Abilities
- Excellent written and oral communication skills with ability to work in cross-disciplinary drug discovery environments.
- Excellent team player that can also work well independently and remote.
- Experience interacting with customers, service engineers, product marketing managers, and R&D.
Compensation and Benefits
The salary range estimated for this position based in New York is $112,500.00–$168,750.00. This position may also be eligible to receive a variable annual bonus based on company, team, and/or individual performance results in accordance with company policy. We offer a comprehensive Total Rewards package that our U.S. colleagues and their families can count on, which includes:
- A choice of national medical and dental plans, and a national vision plan, including health incentive programs.
- Employee assistance and family support programs, including commuter benefits and tuition reimbursement.
- At least 120 hours paid time off (PTO), 10 paid holidays annually, paid parental leave (3 weeks for bonding and 8 weeks for caregiver leave), accident and life insurance, and short- and long-term disability in accordance with company policy.
- Retirement and savings programs, such as our competitive 401(k) U.S. retirement savings plan.
- Employees’ Stock Purchase Plan (ESPP) offers eligible colleagues the opportunity to purchase company stock at a discount.
For more information on our benefits, please visit: https://jobs.thermofisher.com/global/en/total-rewards
See All 68 Application Engineer Jobs in New York
Find roles in New York that match your experience and apply in just a few clicks.
Find Application Engineer JobsApplication Engineer Jobs by City in New York
Where New York roles are concentrated, by current openings.
Application Engineer Job Market in New York
A snapshot from current New York openings, updated as new roles post.
Who's Hiring
- Genpact9

- City of New York4

- Palantir Technologies3

- Bank of China USA2

- Capgemini2

Top Industries Hiring
- Technology & Software21
- Consulting & Professional Services7
- Investment & Asset Management7
- Law & Legal Services7
- Government & Public Sector6
What New York Employers Look For
The qualifications that appear most often in application engineer jobs across New York.
- Bachelor's degree in electrical, mechanical, computer, or systems engineering required
- Hands-on experience with application development, integration, or technical customer support
- Proficiency with relevant platforms such as SaaS products, PLCs, or embedded systems
- Strong ability to deliver technical presentations and product demonstrations to customers
- Experience collaborating with sales, product, and engineering teams on customer solutions
- Familiarity with CRM tools and structured troubleshooting or escalation workflows
Application Engineer Jobs in New York: Frequently Asked Questions
How do you become a application engineer in New York?
Most application engineer roles in New York require a bachelor's degree in an engineering discipline such as electrical, mechanical, computer, or systems engineering. New York does not impose a state-issued license specific to application engineers, though roles in certain regulated industries may require a Professional Engineer registration through the New York State Education Department's Office of the Professions. Employers in sectors like industrial automation or defense often expect relevant technical certifications alongside a degree.
Which companies hire application engineers in New York?
Employers hiring application engineers in New York right now include Genpact, City of New York, and Palantir Technologies, based on current listings on Migrate Mate as of June 2026. New York's concentration of technology, manufacturing, and financial services firms means openings are especially active across enterprise software, automation systems, and semiconductor companies with regional offices or headquarters in the state.
Which New York cities have the most application engineer jobs?
The cities with the most application engineer openings in New York are New York, Buffalo, and Rochester. New York City dominates due to its dense technology and financial services industries, while Long Island draws openings from aerospace and defense contractors, and mid-state hubs like Albany and the Hudson Valley attract roles from semiconductor manufacturing and industrial automation firms anchored in those regions.
Are there remote application engineer jobs in New York?
Yes, and more than many technical roles, because application engineers working on software integration, SaaS platforms, or cloud-based systems can often perform demos, onboarding, and support work entirely off-site. About 35% of application engineer openings tied to New York are remote or hybrid as of June 2026, reflecting real flexibility in the software-facing side of the role. Hardware-focused or manufacturing-embedded positions remain predominantly on-site.
How can I get hired as a application engineer in New York with little or no experience?
The most realistic entry path is through associate application engineer or technical support engineer roles, which large New York employers use as structured on-ramps for recent graduates. Companies in Long Island's aerospace sector and New York City's enterprise software market regularly hire new graduates into rotational or junior application roles. A degree in an engineering discipline, a strong capstone or internship project, and any platform-specific certification such as a vendor-issued credential in automation or cloud software will give a candidate a competitive edge over other early-career applicants.
Where can I find and apply to application engineer jobs in New York?
You can find and apply to application engineer jobs in New York on Migrate Mate, which lists current openings across New York City, Long Island, and the Hudson Valley. Search the listings, find roles that fit your background and target location, and apply directly through the posting.
See All 68 Application Engineer Jobs in New York
Find roles in New York that match your experience and apply in just a few clicks.
Find Application Engineer Jobs