This study presents an experimentally informed three-dimensional finite element muscle model to investigate the influence of aponeurosis thickness on muscle mechanics and injury mechanisms. To capture muscle architecture and aponeurosis geometry, two rabbit soleus muscles were used: one for surface reconstruction and muscle fascicle digitization, and one to quantify aponeurosis thickness. Using these experimental data, we developed a finite element muscle model enabling simulations of isometric contraction, passive lengthening, and active lengthening. To quantify the impact of alternative aponeurosis thickness representations, models with a constant thickness, a linear thickness reduction, and an experimentally based thickness distribution were configured. Model simulations show maximal strains at the aponeurosis–muscle junction and a strong dependence of fibre stretch and strain patterns on the aponeurosis thickness representation. These findings highlight aponeurosis thickness as a critical factor that should be explicitly considered in simulation studies aimed at understanding injury mechanisms and overall muscle function.