A three-dimensional progressive damage model has been developed to capture the onset and initial propagation of damage within a three-dimensional woven composite in a single-bolt, double-shear joint. Reinforced with a three-dimensional woven ply to ply interlock IM7 carbon fiber preform impregnated with toughened epoxy resin and manufactured using a resin transfer molding process, the composite represents a unique material currently used in select aerospace structures. The modeled joint is commonly found in many aerospace structures and, when combined with the progressive damage response of this three-dimensional woven composite, the material response can be reliably predicted with a three-dimensional non-linear finite element model. This model is constructed using an orthotropic material assumption far from the bearing area and a voxelized mesoscale model with an as-molded geometry representing matrix and impregnated tow phases. The well-established Hashin failure criteria and the Matzenmiller–Lubliner–Taylor damage model were implemented with the unique morphology of three-dimensional woven composites. The onset of damage and trends seen in the model were found to be in agreement with previous experimental findings