To investigate the fatigue performance of vertical web stiffener to deck plate welded joints in weathering steel box girders, six specimens of the weathering steel (WS) Q345qNH, four specimens of WS Q420qNH, and four specimens of the plain carbon steel (CS) Q345q for comparison were tested by a vibratory fatigue testing machine, considering different steel grades, yield strengths, stiffener plate thicknesses, and weld types. The fatigue strength was evaluated based on S-N curves and the crack propagation was analyzed by linear elastic fracture mechanics (LEFM). The results show that the fatigue crack of the welded joints was initiated from the end weld toe of the deck plate and subsequently propagated both along the thickness of the deck plate and in the direction perpendicular to the stiffener plate. The fatigue crack initiation and propagation life of WS Q345qNH specimens were longer than those of CS Q345q specimens. The fatigue crack propagation life of WS Q345qNH specimens was longer than that of WS Q420qNH specimens, while the initiation life bore little relationship to the yield strength. Increasing the stiffener plate thickness effectively delayed crack initiation and slowed down its propagation. Compared with fillet welds, full penetration welds extended the fatigue crack propagation life, while no significant improvement was implied for the initiation life. The WS and CS specimens could be classified as having the same fatigue strengths by nominal stress, hot spot stress, and effective notch stress approaches, which were FAT 50, FAT 100, and FAT 225, respectively. Meanwhile, their material constants for LEFM were relatively close to each other.