The refill friction stir spot welding (refill FSSW) process is an innovative solid-state spot-welding method, which has evolved from the concept of friction stir welding. Compared to riveting, the process has the advantage of avoiding stress concentration by eliminating holes. In addition, weight can be saved compared to riveting as no additional material is needed. However, the fatigue strength of refill FSSW joints under cyclic loading is still not satisfactory. To address this challenge, laser shock peening (LSP) is investigated as an innovative residual stress engineering technique to improve the fatigue performance of refill FSSW AA2024-T3 joints. Two application scenarios are investigated, one investigating the LSP technique as a complementary manufacturing process to the refill FSSW technology, and the other investigating the LSP technique as a repair process for damaged joints. The fatigue test results showed that the application of the LSP treatment can significantly improve the fatigue behaviour of the refill FSSW overlap joints. In terms of Basquin fatigue strength, the LSP treatment resulted in an improvement by a factor of 1.51 and 2.82 for the one- and two-sided LSP-treated specimens, respectively. The life of specimens with refill FSSW joints that had been specifically pre-damaged by stopping the fatigue test at approximately 51%, 75% and 83% of the number of cycles to the Basquin fatigue strength, applying LSP treatment and continuing the fatigue test was also significantly extended. The results of this study show that LSP is a very effective technique for significantly extending the fatigue life of refill FSSW joints. Therefore, the combination of these two manufacturing processes, refill FSSW and LSP, represents a promising technology for industrial companies that require high fatigue performance for their structural components.