Friction stir welding (FSW) has shown considerable promise for highway aluminum bridge deck fabrication but lacks specific quality control guidelines for fit-up defects. This study conducts a performance-based (PB) quality control assessment of butt-lap FSW joints for highway bridge decks. Five FSW conditions were simulated, including a standard control welding condition, fit-up defects (gaps and tool offset), and a welding tool’s rotational direction inversion from the standard condition. A rigorous prequalification process established acceptable tolerance levels for fit-up defects: a 3 mm positive offset, a 1.5 mm negative offset, and a 1.5 mm gap. Subsequently, specimens from real aluminium deck extrusions, incorporating the various welding conditions were subjected to fatigue testing. Results showed that the fatigue strength and failure mode were primarily influenced by the weld root microstructure. The FSW tool’s rotational direction significantly influenced fatigue strength due to its impact on the nucleation of the hooking defect in the weld root area, while the impact of fit-up defects on fatigue strength was comparatively lesser. Furthermore, finite element analysis examined the impact of the geometrical features of the root microstructure and the direction of the initial crack propagation on the stress intensity factor range. These findings have practical implications for setting tolerance levels for fit-up defects in aluminum butt-lap FSW joints and optimizing of the quality and fatigue strength of butt-lap FSW joints.