Application Engineer Jobs in San Francisco, CA
Application Engineer jobs in San Francisco are concentrated in SoMa, the Financial District, and Mission Bay, driven by enterprise software, cloud infrastructure, and life sciences employers. Companies currently hiring include Rippling, OpenAI, and Airwallex. Find a role that fits below and apply directly.
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INTRODUCTION
The APeX Application Analyst functions as the primary support contact and expert for the application. They work under the direction of the Team Lead and/or Manager to configure, build & install the application. They coordinate all issues that arise during the project for their application area. Key operational activities include primary responsibility to analyze work flows and understand policies, procedures and constraints of the clinical or business operations supported by the application. In depth and precise investigation and documentation of operational specifications and application functionality is required. Key technical activities include the analysis of new releases to determine how workflow should be modified, building and populating databases and tables during initial system configuration, conducting system testing and conversion data validation. The application analyst develops and documents internal procedures and establishes change control processes for the application.
The APeX Application Analyst also develops user training aids and trains end users in workflow and use of the application. They function as the primary contact to troubleshoot problems and questions from end-users during training, go-live, stabilization and ongoing support (7x24). Successful candidates are skilled communicators who make decisions independently and in collaboration with others up and down the project structure. They are considered technical leaders with a high degree of knowledge in the overall field and recognized expertise in specific areas. Attention to detail is a critical skill for this position. Successful candidates enjoy helping other users to learn and adopt to use of the application.
In addition to general system support and maintenance, this position will be heavily involved in areas of medication billing including but not limited to processing medication receiving, billing error resolution, medication cost updates, 340b build maintenance, HCPC maintenance, and follow up to billing related inquiries. Past experience as a Willow Analyst in these areas or experience in hospital medication charging are preferred.
The APeX Application Analyst – Willow must be certified in one of the following APeX applications (or successfully receive certification within 6 months of hire):
- Willow
Department Overview
The Clinical Applications Team is responsible for designing, testing, and implementing the clinical aspects of UCSF’s Electronic Health Record. Includes interoperability with other third party systems and devices.
Our Core Values include:
Judgment: Makes wise decisions, root causes, thinks strategically, and prioritizes what to do now and what can be improved later.
Communication: Listens well, concise and articulate in speech and writing, treats people with respect independent of their status or disagreement with you & maintains calm poise in stressful situations.
Impact: Accomplish amazing amounts of important work, colleagues can rely upon you, focus on results, exhibit bias-to-action, and avoid analysis-paralysis.
Innovation: Find practical solutions to hard problems, suggest better approaches, new ideas that prove useful, stay nimble by minimizing complexity and finding time to simplify.
REQUIRED QUALIFICATIONS
- Bachelor's degree in health care information technology, computer science, or related area, and/or equivalent combination of experience/training.
- Three years of relevant work experience.
- Uncertified candidates must obtain Epic certification within 6 months of hire.
- Broad and/or in-depth knowledge of 1-2 areas of focus in clinical applications specialty area(s). Knowledge of systems and functions, including design, development, implementation, user support and training, maintenance, quality assurance, and system testing and evaluation.
- Strong problem-resolution skills, with the ability to quickly diagnose problems, and develop, test, and implement appropriate and effective solutions in a timely manner.
- Strong interpersonal skills, with the ability to effectively train, support, and work collaboratively with users of clinical information systems at all professional and technical levels.
- Detail-oriented, with proven organizational skills and the ability to effectively manage time, prioritize tasks, and see projects through to completion on deadline.
- Strong written and verbal communication skills, with the ability to convey technical information and instructions to all levels of clinical applications users in a specific, clear, and concise manner.
- Strong analytical skills and knowledge in documentation and reporting, with the ability to design and execute tests, analyze system performance data, and produce substantive reports and analyses.
- Ability to work with senior staff and managers, serving as a technical resource and providing advice and counsel on issues of functionality, efficiency, cost-effectiveness, policy, and performance.
PREFERRED QUALIFICATIONS
- Academic Medical Center experience with 3+ years of Epic experience.
- Experience in Willow medication billing build/support or in hospital medication charging functions.
- Epic Willow Application Certification.
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Find Application Engineer JobsApplication Engineer Job Market in San Francisco
Who's Hiring
- Rippling19

- OpenAI13

- Airwallex8

- Anthropic8

- CLERA5C
Top Industries Hiring
- Technology & Software136
- Science & Research25
- Banking & Financial Services12
- Consulting & Professional Services11
- Fintech7
Application Engineer Jobs in San Francisco: Frequently Asked Questions
How do I get a application engineer job in San Francisco?
Target the enterprise software, cloud, and biotech companies concentrated in SoMa, Mission Bay, and the Financial District, where demand for application engineers is highest. Hands-on experience with APIs, systems integration, or customer-facing technical implementations gives you a clear edge. Candidates who can demonstrate pre-sales or post-sales technical support experience tend to move quickly through hiring pipelines at San Francisco's fast-moving tech and life sciences firms.
Which companies hire application engineers in San Francisco?
San Francisco application engineer roles are posted by Rippling, OpenAI, and Airwallex and others right now, based on current listings on Migrate Mate as of June 2026. The city draws a mix of large enterprise software vendors, early-stage startups, and medical device or biotech firms, all of which rely on application engineers to bridge technical products and customer needs.
Are there remote application engineer jobs in San Francisco?
Yes, though availability depends heavily on the role: customer-facing and integration-heavy positions typically require on-site or hybrid presence, while more analytical or documentation-focused work can run fully remote. About 37% of application engineer openings tied to San Francisco are remote or hybrid as of June 2026. Product support and pre-sales engineering roles at San Francisco software companies represent the largest share of those flexible arrangements.
How can I get a application engineer job in San Francisco with little or no experience?
The most realistic entry path in San Francisco is through junior technical support or solutions engineer roles at mid-stage SaaS companies in SoMa or the Financial District, where structured onboarding is more common. Bootcamp graduates and candidates with strong API or scripting fundamentals are regularly considered for associate-level positions. Targeting companies that sell complex software to enterprise clients gives you the best chance, since those teams need people who can learn a product deeply and explain it clearly.
Which industries hire the most application engineers in San Francisco?
The sectors hiring the most application engineers in San Francisco are Technology & Software, Science & Research, and Banking & Financial Services, based on current listings on Migrate Mate as of June 2026. San Francisco's dense concentration of enterprise software headquarters, cloud infrastructure companies, and life sciences campuses in Mission Bay creates sustained, year-round demand for technical roles that sit between product and customer.
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