The fatigue crack propagation in a friction stir‐welded sample has been simulated herein by means of two 3‐dimensional finite element method (FEM)‐based analyses. Numerical simulations of the fatigue crack propagation have been carried out by assuming a residual stress field as a starting condition. Two initial cracks, observed in the real specimen, have been assessed experimentally by performing fatigue tests on the welded sample. Hence, the same cracks have been placed in the corresponding FE model, and then a remote load with boundary conditions has been applied on the welded specimen. The material behaviour of the welded joint has been modelled by means of the Ramberg‐Osgood equation, while the non‐linear Kujawski‐Ellyin (KE) model has been adopted for the fatigue crack propagation under small‐scale yielding (SSY) conditions. Owing to the compressive nature of the residual stress field that acts on a part of the cracked regions, the crack closure phenomenon has also been considered. Then, the original version of the KE law has been modified to fully include the closure effect in the analysis. Later, the crack closure effect has also been assessed in the simulation of fatigue propagation of three cracks. Finally, an investigation of the fracture process zone (FPZ) extension as well as the cyclic plastic zone (CPZ) and monotonic plastic zone (MPZ) extensions have been assessed.