Cohesive Zone Models with finite thickness are widely used for the fracture mechanical modeling of material layers, e.g., adhesive layers. Within this approach, the whole layer is modeled as a cohesive zone. Moreover, computational homogenization techniques are crucial for the development of advanced engineering materials, which are often heterogeneous. Compared to the commonly used Finite Element Method (FEM), solvers based on the Fast Fourier Transform (FFT) are expected to reduce the computational effort needed for the homogenization. Originated from an existing method for the computational homogenization of cohesive zones using FEM, a novel FFT-based homogenization scheme for cohesive zone models is presented. Our implementation of the FFT solver uses a displacement-based Barzilai–Borwein scheme and a non-local ductile damage model for the fracture behavior. Finally, the practical application of the method is discussed using an adhesive layer and the core material of HybrixTM metal sandwich plates as examples.