Optimization of aircraft's performance often requires careful consideration of aerodynamic drag. However, direct measurement of drag of a flying vehicle is not feasible. Therefore, in order to measure the change in drag for different configurations of a flying aircraft, in-flight thrust measurement is necessary, which can consequently be used to derive drag. For this reason, the design of an in-flight thrust measurement system for a pylon-mounted jet engine is presented. The system is based on the trunnion thrust method. The design process is described, including a review of state of the art as well as measurement error consideration. Calibration methods are presented. During the calibration, the thrust root-mean-square error of 0.64 N was observed. The system was flight tested and proved to work reliably in real-life conditions. Finally, the flight test data was used to generate a thrust model based on engine parameters.