This paper describes the structure and application of a software system that automates the fatigue initiation and crack propagation analysis based on finite element method (FEM). The system automatically performs necessary procedures to track propagation history of cracks: insertion of a crack and updating of three-dimensional (3D) finite element mesh in accordance with the crack propagation. The system is equipped with a function to automatically perform fatigue analyses using the stress–strain histories at nodes of a 3D FEM model. Some analyses for several examples were carried out for validation. The important example is the surface crack propagation in steel pipes with residual stress.