Physical activity is crucial for the quality of life of individuals with disabilities. In many parasports, such as wheelchair basketball, the wheelchair is an essential component. However, the repetitive nature of wheelchair propulsion frequently leads to overuse injuries, with the shoulder being the most commonly affected joint. The aim of this study was to assess the intensity of shoulder pain in wheelchair basketball players in Benin at three time points: before a championship, immediately after the championship, and following a subsequent 3-month rest period, using the Wheelchair User’s Shoulder Pain Index (WUSPI). This prospective observational study included 10 elite male wheelchair basketball players (mean age: 32 ± 5 years; mean experience: 13 ± 8 years). The WUSPI was administered at pre-championship (T0), post-championship (T1), and after a 3-month rest period (T2) to assess shoulder pain intensity during activities of daily living (ADLs). The Friedman test and post-hoc Wilcoxon signed-rank tests were used to compare scores between time points. The mean performance-corrected WUSPI (PC-WUSPI) score increased significantly from baseline at T0 (13.45 ± 5.77) to T1 (69.88 ± 21.91) (p < 0.001). Following the rest period, the score at T2 (43.92 ± 20.0) was significantly lower than at T1 (p < 0.001). However, the T2 score remained significantly higher than the initial baseline score at T0 (p < 0.001). Intensive competition induces a substantial increase in shoulder pain and functional limitation in elite wheelchair basketball players. While a 3-month rest period allows for significant pain reduction, recovery is incomplete, with pain levels remaining elevated above pre-competition baseline. These findings highlight the high physical demands of the sport and underscore the need for targeted pain management and recovery strategies.