A multiaxial fatigue criterion recently developed by the authors for 2D conditions is extended here to 3D situations and applied to predict fatigue damage in rail welded joints with the help of an explicit finite element model. Contact theory and axle box acceleration response in frequency domain are used to validate the finite element model. The influence of depth and length of the welded joints is analyzed. It is found that fatigue damage is more severe with shorter and deeper welded joints. When the length of the welded joints is less than 150 mm, fatigue damage is greatly increased with the increasing of the depth. When the depth is less than 0.1 mm, fatigue damage is not relevant, regardless of the length. When the depth is greater than 0.3 mm, fatigue damage increases significantly with the decreasing of the joint length, especially when the length is less than 150 mm. When the welded joints are long enough, the depth restriction can be relaxed. This work can provide guidance and theoretical support for maintenance and repair of rail welded joints.