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Flagship Pioneering, Inc.
Actively hiring

Senior UAS Systems Integration Engineer II

Workplace
On-site
Commitment
Full-time
Seniority
Senior
Salary
$95,000-130,000/yr
Posted
Location
Cambridge, United StatesBoulder, United States

This role joins Flagship Pioneering's growing hardware team as a UAS Systems Integration Engineer II, working at the intersection of firmware, electronics, and airframe design. The engineer will help drive the technical architecture of a 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, the role moves 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.

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.

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; PCB design and fabrication 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;
  • 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 have

  • 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;

Benefits

  • 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.