The fatigue characteristics of glass fiber reinforced plastic (GFRP) composites were studied under repeated loads using the finite element method (FEM). To realize the material characteristics of GFRP composites, Digimat, a mean-field homogenization tool, was employed. Additionally, the micro-structures and material models of GFRP composites were defined with it to predict the fatigue behavior of composites more realistically. Specifically, the fatigue characteristics of polybutylene terephthalate with short fiber fractions of 30wt% were investigated with respect to fiber orientation, stress ratio, and thickness. The injection analysis was conducted using Moldflow software to obtain the information on fiber orientations. It was mapped over FEM concerned with fatigue specimens. LS-DYNA, a typical finite element commercial software, was used in the coupled analysis of Digimat to calculate the stress amplitude of composites. FEMFAT software consisting of various numerical material models was used to predict the fatigue life. The results of coupled analysis of linear and nonlinear material models of Digimat were analyzed to identify the fatigue characteristics of GFRP composites using FEMFAT. Neuber’s rule was applied to the linear material model to analyze the fatigue behavior in LCF regimen. Additionally, to evaluate the morphological and mechanical structure of GFRP composites, the coupled and fatigue analysis were conducted in terms of thickness.