In this study, the effect of repair welding on the fatigue behavior of AA6082-T6 welded T-joints in marine structures was investigated based on experiments and the fitness-for-service (FFS) assessment in BS7910. Repair welding led to an increase in residual stress and a decline in fatigue life according to fatigue tests and FEA. Meanwhile, repair welding changed the crack initiation site (CIS) and crack shape factor (CSF, the ratio of crack depth a to length 2c; i.e., a/2c), as indicated by fatigue fractography. In addition, when FFS assessment was performed, two methods for characterizing the CSF under different repair welding lengths during fatigue crack growth were presented: fixed and non-fixed a/2c. The results showed that repair welding led to a transition from ductile fracture to brittle fracture. For a fixed CSF, the critical crack depth and crack opening area of T-joints with repair welding lengths of 30 mm were greatly reduced by 63–66% and 86–89%, respectively, compared to T-joints without repair welding. However, the corresponding reductions for the non-fixed a/2c method were approximately 40% and 90%. The comparison indicated the results obtained with a non-fixed CSF were more consistent with the experiments, with a deviation below 15%.