The article deals with the development of a highaccuracy flight controller for the uncrewed vehicles (UVs) based on the MDR32F9Q2I microcontroller with the integration of the UM982 module of the global navigation satellite system (GNSS). The development includes adaptation of resource-intensive GNSS data processing algorithms to the microcontroller restrictions (128 KB Flash, 80 MHz) using fixed-point arithmetic and the peculiarities of microcontroller’s system interrupts. We propose to study the integration algorithms for navigating the UVs based on the developed flight controller prototype. We consider the task of clarifying the coordinates of the inertial navigation system based on the GNSS data. The implemented hardware and software platform opens up prospects for its transfer to heterogeneous UVs.