Structural stress approach is well known as a mesh-size insensitive fatigue assessment method by using finite element analyses. It is, however, difficult to estimate the structural stress (SS) at weld end points due to stress singularities when shell elements are used. In this study, fatigue evaluations with longitudinal load carrying box fillet weldment under out-of-plane bending load have been performed by using virtual node method (VNM) in order to avoid the problem, which is called the weld end effect. Various combinations of virtual node parameters, such as reference point and virtual node locations, are investigated for the estimation of proper structural stress values applying VNM in a systematic manner. The appropriate guidance of virtual node parameter has been offered for the fillet weldment considered in the study. The structural stress values obtained by VNM have also been validated by comparing the result with finite element model including weld bead. Moreover, the fatigue strength of the fillet weldment based on the equivalent structural stress is shown to be consistent with the master S-N curve.