This paper deals with the fatigue strnegth of electron beam welded joint made from the welding structure steel SM41. The cause of the difference in the fatigue strength between electron beam (EBW) and CO2 gas (CO2W) welded joints was investigated by comparing the factors which are the weld reinforcement, the residual stress and the hardness at the neighbourhood of the toe. The fatigue strength of CO2W welded joint was considerably lower than that of the base metal, but the fatigue strength of EBW welded joint was equal to that of the base metal in order to occur fracture in the base metal of EBW welded joint. Therefore, above factors of jonits welded by both welding processes were studied. The values of residual stress in the fatigue specimen machined from the welded joint were nearly zero. The stress concentration factor calculated from the weld reinforcement geometry of EBW was smaller than that of CO2W. The hardness at the toe of EBW welded joint was extremely larger than that of CO2W welded joint. The fatigue test results of notched specimens quenched by high frequency and non-quenched suggested that the difference of the fatigue strength between EBW and CO2W welded joints was caused by both the increasing hardness and the decreasing the stress concentration factor.