Senior UAS Systems Integration Engineer II

COMPANY DESCRIPTION

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 company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies.   

What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet.   

Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. 

THE ROLE

We are seeking a UAS Systems Integration Engineer II to join our growing hardware team. This is a deeply technical, hands-on engineering role for someone who lives at the intersection of firmware, electronics, and airframe design. You will help drive the development of the technical architecture of our fixed-wing UAV platform — co-developing the autopilot stack, airframe, payload integration, and C2 link from the ground up. Working within a small, high-caliber team, you will drive the system from early prototype toward a hardened, field-deployable platform capable of executing precision scientific missions in demanding international environments. The ideal candidate brings end-to-end systems thinking and a builder's instinct — equally comfortable in CAD, oscilloscope traces, and firmware source code.

KEY RESPONSIBILITIES

• Configure, tune, and iterate on autopilot firmware for fixed-wing airframes, including PID tuning, failsafe logic, auto modes, and mission scripting using ArduPlane;
• Read, modify, and debug ArduPilot source code (C++) to extend autopilot capabilities, implement custom behaviors, and resolve vehicle-level anomalies;
• Design, build, and iterate on fixed-wing airframes across aerodynamics, structures, and propulsion integration — optimized for payload capacity, endurance, and operational resilience;
• Support flight test campaigns alongside flight operations — pre-flight vehicle readiness checks, ground station and telemetry setup, in-field troubleshooting, and rapid turnaround of firmware and hardware fixes between flights;
• Develop C2 link architecture, RF link budgets, electronics integration, and spectrum compliance strategies for long-range BVLOS operations;
• Design and implement custom ground station software and user interfaces to support mission planning, real-time monitoring, and post-flight analysis;
• Integrate and validate onboard science payloads and sensors, ensuring electrical compatibility, data integrity, and mission performance;
• Analyze flight logs (MAVExplorer, Flight Review) to diagnose anomalies, validate performance models, and drive systematic improvements to vehicle reliability;
• Design and fabricate custom electronics, including PCB layout for power distribution, sensor interfacing, and avionics integration;
• Document designs, test results, firmware change logs, and component specifications to build a scalable engineering knowledge base for the drone program.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Bachelor's or Master's degree in aerospace engineering, electrical engineering, mechanical engineering, computer science, or a closely related field; equivalent hands-on experience will be considered.
  • BS + 2-4 or MS + 0-2 years of hands-on hardware/software systems integration experience required, in real-mission or production contexts;
• Proficiency in C++ and Python, with demonstrated experience reading, modifying, and debugging ArduPilot source code; strong familiarity with MAVLink protocol and GCS tooling;
• Hands-on experience with ArduPilot or PX4 based autopilot systems, preferably in production-ready or real-mission contexts;
• Experience with RF link design, C2 spectrum compliance, antenna selection, and electronics integration for long-range UAV systems;
• Electronics design and integration experience required; PCB design and fabrication experience is a strong plus;
• FAA Part 107 Remote Pilot Certificate is a plus (or the ability to obtain is required); BVLOS waiver experience is a strong plus;
• Ability to work hands-on across the full hardware stack — from firmware and avionics to airframe fabrication and field deployment — in a small team environment;
• Experience with atmospheric sensing instrumentation or science payload integration is a strong plus;
• Strong documentation and engineering rigor: changelogs, test reports, design rationale, and component specifications suitable for future scaling and external review;
• Genuine passion for building novel aerial systems with real-world scientific impact, and comfort operating at the frontier of hardware, firmware, and systems engineering.

LOCATION:  Boulder, CO

ABOUT FLAGSHIP PIONEERING:

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  

Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

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 of the experience listed above but not all, 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.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

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The salary range for this role is $95,000 - $130,000. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Protocos currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Protocos's good faith estimate as of the date of publication and may be modified in the future.