The paper is devoted to study unmanned aerial vehicle (UAV) flight operational features and UAV’s automatic control system operating in manual mode (it processes pilot’s control commands). The analysis of operation in special cases and conditions is carried out for the aircraft equipped with a radio-operating human-controlled system and automatic flight control system. The main goal of the research is to develop fully functional flight controller the flight controller based on the domestic made microcontroller unit (MCU) MDR 32. The main novelty is that board LDM-BB-K1986BE92QI with the MDR32F9Q2I microcontroller core is used as a hardware base for the flight controller. The development of hardware and software are described separately including some features that was used to overcome several limitations of the selected MCU. The base flight controller firmware modules, functions and algorithms are described. A sample quadrotor based on the S550 frame was assembled using the developed flight controller to carry out testing flights. Two test experiments are presented: the first one is a checking of the flight controller base functionality (parameters configuration and calibration) and the second one is a test flight performed by a pilot.