The effect of High-Frequency Mechanical Impact (HFMI) treatment on the fatigue resistance of structural steel S355 butt welds with macro geometric imperfections outside of the usual fatigue design limits was investigated. Thin-walled specimens (t = 8 mm) were manufactured with different degrees of angular and linear misalignment and fatigue tested in the as welded and HFMI treated condition. The fatigue test results show that HFMI treatment can compensate the fatigue strength-reducing effects of macro geometric imperfections (ΔσC,HFMI = 127 N/mm2, m = 5), but also that linear and angular misalignment does not reduce the fatigue strength of butt welds as severely as rules and guidelines suggest (ΔσC,AW = 107 N/mm2, m = 3). Underestimating the fatigue strength determined by testing by more than 40%, numerical analysis and strain gauge measurements show that the application of the effective notch stress approach and the structural hot-spot stress approach delivers conservative assessment results, which might not always be representative for the actual fatigue strength benefit that can be gained by HFMI treatment.