Senior UAS Systems Integration Engineer II

Boulder, CO USA

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.

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.

• Configure, tune, and iterate on autopilot firmware for fixed-wing airframes, including PID tuning, failsafe logic, auto modes, and mission scripting using Ardu Plane;
• Read, modify, and debug Ardu Pilot 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…