The aim of this study was to analyze whether a compensatory training program, including isoinertial flywheel training, could reduce shoulder imbalances in a group of asymptomatic young tennis players. After an initial evaluation, 26 young tennis players were assigned to either a supervised flywheel training group (FTG, n = 13) or a control group (CG, n = 13). Shoulder passive internal (IR) and external rotation (ER) range of motion (ROM) as well as shoulder IR and ER maximal isometric strength were measured before and after a 12-week training intervention, performed 3 times per week. After the intervention, results showed significant changes for IR (p < 0.001, effect size [ES] = 1.83) and ER (p < 0.001, ES = 1.77) on the dominant (D) side, and IR on the nondominant (ND) side (p < 0.001, ES = 2.24) in the FTG compared with the CG. Regarding the ROM values, results showed that the FTG achieved significantly greater increases for the IR ROM (p < 0.001, ES = 3.32) and total ROM (TROM) (p = 0.004, ES = 1.39) on the D and ND sides (IR ROM: p = 0.002, ES = 1.53; TROM: p < 0.001, ES = 2.35) than the CG. Moreover, the CG displayed larger decrements in ER ROM (p = 0.016, ES = 1.12) on the ND side after the training period than the FTG. The conducted compensatory training program was effective to increase the ER strength and IR mobility of the FTG players, which led to a reduction in the glenohumeral imbalances.