During the modernization of the low-pressure compressor of the regional aircraft engine, a flow separator made of polymer composite material was developed, which has less weight, is easier and cheaper to manufacture. However, the separator must undergo a series of tests before being installed on the engine, in particular the endurance tests, necessary to assess the fatigue strength margin. A method for determining the endurance limit of a large part of an aircraft engine is developed in the presented work and consists in replacing the tests of the entire separator with tests of individual structural elements cut from the part. The shape, dimensions and fixation of the elements have been chosen in such a way that their own test frequency was close to the natural frequency of the flow separator on the engine. The natural oscillation frequencies and places of maximum dynamic stresses have been determined before testing on three-dimensional models of the flow separator and elements cut from it. As a result, the structural elements have been tested until appearance of fatigue cracks which allowed to assess the endurance limit and evaluate fatigue strength margin of the separator.