Engineer II, Flight Systems

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 Flight Engineer II to join our growing hardware team. This is a hands-on engineering role focused on fixed-wing UAV development, BVLOS operations planning, and systems integration. You will focus on a critical component of our platform — designing, building, operating, and iterating on a purpose-built aerial system where the airframe, autopilot stack, and payload integration are all co-developed from the ground up. This role will work alongside a small, highly technical team at the intersection of advanced science, cutting-edge engineering, and field operations, moving us from early prototype flights toward a hardened, field-proven platform capable of executing precision missions in demanding international environments.

KEY RESPONSIBILITIES

• 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 suited to a variety of payload designs, working across aerodynamics, structures, and propulsion integration;
• Plan BVLOS operations planning 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 to vehicle performance and reliability;
• Collaborate with the 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 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 and up to 4 years or MS and 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 ArduPilot 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 an understanding of aerodynamic design trade-offs for custom platforms;
• FAA Part 107 Remote Pilot Certificate is a plus (or the ability to obtain 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 changelogs, flight logs, test reports, and component specifications suitable 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.

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.

#LI-TL1

The salary range for this role is $86,000 - $118,200. 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.