Senior UAS Systems Integration Engineer II

Flagship Pioneering, Inc.•Boulder, CO

10h•$95,000 - $130,000•Onsite

About The Position

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.

Requirements

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;
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;
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.

Nice To Haves

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;
Experience with atmospheric sensing instrumentation or science payload integration is a strong plus.

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.