Fatigue crack can be a controlling factor in the life of some welding components, such as vertical and horizontal stiffener. In this study, FE analysis was carried out to examine the three-dimensional fatigue crack penetration of gusset welded joint using the finite element analysis program FEMAP and FRANC3D. Three-dimensional fatigue crack penetration analysis result was compared with two dimensional fatigue crack penetration analysis result. From the FE analysis results, stress intensity factor(SIF) and crack propagation cycles were evaluated.