Protocos | Boulder, CO Engineer, Flight Systems

About Flagship Pioneering

Flagship Pioneering is a platform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial builders and assemble capital to enable courageous leaps in areas such as human health, sustainability, and AI‑driven technologies.

We are seeking a UAS Flight Engineer II to join our growing hardware team. This hands‑on engineering role focuses on fixed‑wing UAV development, BVLOS operations planning, and systems integration. You will design, build, operate, and iterate a purpose‑built aerial system where the airframe, autopilot stack, and payload integration are co‑developed.

• Configure, tune, and iterate on autopilot firmware for fixed‑wing airframes, including PID tuning, failsafe logic, auto modes, and mission scripting.
• Design, build, and iterate on fixed‑wing airframes for a variety of payloads, integrating aerodynamics, structures, and propulsion.
• Plan BVLOS operations and flight test execution, including waiver compliance, pre‑flight risk assessment, and real‑time mission monitoring.
• Develop C2 link architecture, RF link budget, electronics integration, and spectrum compliance for long‑range operations.
• Design software for custom ground station capabilities and user interfaces.
• Analyze flight logs (MAVExplorer, Flight Review) to diagnose anomalies and drive iterative improvements.
• Collaborate with science and field teams to integrate and validate onboard sensors, ensuring data quality and mission success.
• Document designs, test results, and standard operating procedures to build a scalable engineering knowledge base.

• Bachelor’s or Master’s degree in aerospace, electrical, mechanical engineering, computer science, or a closely related field; equivalent hands‑on experience will be considered.
• BS up to 4 years or MS up to 2 years of hands‑on experience with Ardupilot‑based autopilot systems, preferably in production‑ready or real‑mission contexts.
• Proficiency in C++ and/or Python with experience reading, modifying, and debugging Ardu Pilot source code; familiarity with MAVLink protocol and GCS software (Mission Planner, QGroundControl).
• Practical fixed‑wing airframe build and flight test experience, including manual RC aircraft proficiency and aerodynamic design trade‑offs for custom platforms.
• FAA Part 107 Remote Pilot Certificate is a plus (or the ability to obtain one is required). Experience with BVLOS waivers, 107 Waivers, COA applications, manned aircraft operations, or international UAS regulations is a strong plus.
• Experience with RF link design, C2 spectrum compliance, antenna selection, and electronics integration for long‑range UAV systems.
• Electronics design, integration, and PCB design is a strong plus.
• Experience with atmospheric sensing, meteorology, or weather forecasting is a strong plus.
• Ability to work hands‑on across the full hardware stack in a small team environment—from firmware and electronics to airframe fabrication and field deployment.
• Strong documentation habits, including maintaining change logs, flight logs, test reports, and component specifications for future scaling and external review.
• Experience supporting field campaigns or flight tests in remote or international environments is a plus.
• Genuine passion for building novel aerial platforms with real‑world scientific or environmental impact, and comfort working at the intersection of hardware, firmware, and field operations.

Boulder, CO

Salary range: $86,000 – $118,200. Compensation will depend on qualifications, skills, and experience. Benefits include healthcare coverage, an annual incentive program, retirement benefits, and other perks.

We are an equal opportunity employer. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some, but not all, of the experience listed above, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.