Purpose: To evaluate changes in physical performance indicators after executing a flywheel or machine-based neuromuscular training program in young female tennis players. Methods: Twenty-four players were divided into a machine-based group (MG), flywheel group (FG), and control group. Countermovement jump (CMJ), sprint time (5, 10, and 15 m), change-of-direction (COD) performance (right and left), medicine-ball throws (overhead, forehand, and backhand), and serve velocity were included as tests at baseline, week 4, and week 8. Results: Both MG and FG largely improved from baseline to weeks 4 and 8 of training in CMJ (11.6, 10.6%; effect size [ES] = 1.24, 1.95). Also, sprint time 5 m and 10 m, COD performance-right, and COD performance-left improved moderately to very largely at week 4 in MG (−5.0% to −6.2%; ES = −1.79 to −4.19) and FG (−2.9% to −5.1%; ES = −1.13 to −1.64), respectively. Regarding medicine-ball throw, only FG improved moderately to very largely from weeks 4 to 8 in overhead (9.3%; ES = 1.46), forehand (8.0%; ES = 1.08), and backhand (6.1%; ES = 1.15). Serve velocity improved moderately from weeks 4 to 8 in MG (5.8%; ES = 0.87). Conclusions: Four weeks of the tested programs seem sufficient to improve physical determinants in young female participants. Greater improvements in CMJ and medicine-ball throw following flywheel neuromuscular training indicate the importance of including exercises that emphasize the stretch-shortening cycle and involve the entire kinetic chain. Performing the same intervention with no load adjustments may stall or even decrease performance in some parameters from weeks 4 to 8.