Considering the difference between specimens and RD2 axle of C64A freight car, the extrapolated probabilistic fatigue S-N curves of LZ50 axle steel, which include the long life regime of material, are adjusted by introducing a probabilistic fatigue affecting factor, Kaffect. Based on the adjusted curves, fatigue reliability research on the axle at different operating speeds is carried out. It utilizes the fatigue stress spectrums of the axle in two different wheel set states, namely, normal state and scratched state. The fatigue operating life with arbitrary survival probability and confidence is obtained, and the failure rate with given confidence and design fatigue life is also achieved. Analysis results indicate that the unloading groove of existent RD2 axle is the most dangerous part. When the wheel set is in normal state, fatigue life of C64A freight car RD2 axle decreases with the increase of reliability. Furthermore, scratched wheel set shortens the fatigue life strongly. Therefore, inspection and administration of scratched wheel set are significant. The application of wheel set at relatively high scratch level and high operating speed should be restricted.