Background/objectives: This study aimed to compare the effects of bilateral and unilateral flywheel training programs on leg strength, sprint performance, jumping, and change of direction ability in young basketball players. Methods: Twenty-two youth male basketball players were randomly assigned to two groups: the unilateral group (UG; n = 11; age = 15.5 +/- 0.5 years) and the bilateral group (BG; n = 11; age = 15.2 +/- 0.4 years). Both groups participated in a six-week flywheel training intervention (UG: split squat; BG: half squat) alongside their regular basketball activities. Performance measures included change of direction ability (5-0-5 test), knee extension 60 degrees/s leg strength (EX60), bilateral and unilateral countermovement jump heights (CMJ, CMJL, and CMJD), reactive strength index (RSI), and 5 m and 20 m sprint times (SPR5m and SPR20m). A 2 x 2 ANOVA was used to evaluate pre- to post-intervention changes. Results: Significant interaction effects were observed for the 5-0-5 test (F = 13.27; p = 0.02), with pre-post improvements of 8.4% and 13.3% for the BG and UG, respectively. Both groups showed significant CMJ improvements (11.4%, ES = 0.69 for the BG; 14.6%, ES = 1.4 for the UG). The UG demonstrated greater unilateral jump improvements compared to the BG. Significant RSI improvements were found for both groups (BG: 19.6%, ES = 0.95; UG: 19.6%, ES = 0.77). Both groups improved on sprint performance, with the UG showing slightly larger effect sizes. Conclusions: Unilateral flywheel strength training appeared to be a more effective strategy than bilateral training for enhancing strength, sprinting, jumping, and change of direction ability in youth basketball players.