Flexural fatigue tests were conducted on injection-molded short fiber composites, carbon fiber/poly(phenylene ether ketone) (PEK-C) and glass fiber/PEK-C (with addition of polyphenylene sulfide for improving adhesion between matrix and fibers), using four-point bending at stress ratio of 0.1. The fatigue behavior of these materials was presented. By comparing the S-N curves and analyzing the fracture surfaces of the two materials, the similarity and difference of the failure mechanisms in the two materials were discussed. It is shown that the flexural fatigue failure of the studied materials is governed by their respective tensile properties. The matrix yielding is main failure mechanism at high stress, while at lower stress the fatigue properties appear fiber and interface dominated.