The relatively weak fatigue property of electron beam (EB)‐welded joints is one of the key issues restricting their wide application. Herein, the impact of accelerating voltage, specifically the process‐induced nonuniform microstructure, is investigated on the high‐cycle fatigue properties of 15CrMnMoVA steel EB‐welded joints. It is indicated in the results that increasing the accelerating voltage from 120 to 150 kV (150‐specimen) results in a longer fatigue life and an 11.8% improvement in fatigue limit for the welded joint with the locking bottom structure. However, even after removing the locking bottom structure, the fatigue life of the 150‐specimen is still inferior to that of the base metal. The shorter fatigue life is primarily due to stress concentration and premature fatigue failure caused by the nonuniform distribution of grain size and crystallographic orientation across the EB‐welded joint. Thus, further optimization of the welding process is necessary to improve the fatigue reliability of EB‐welded joints by obtaining a more uniform microstructure.