This study aimed to analyze the effect of velocity based-resistance training (RT) with moderate load and few repetitions per set combined with jumps and sprints on physical performance in young soccer players of different ages. A total of 44 elite youth soccer players belonging to three teams participated in this study: an under-16 team (U16, n = 17) and an under-18 team (U18, n = 16) performed maximal velocity RT program for 26 weeks in addition to typical soccer training, whereas an under-21 team (U21, n = 11) did not perform RT. Before and after the training program all players performed: 20-m running sprint (T20); countermovement jump (CMJ); a progressive isoinertial loading test in squat to determine the load which players elicited ∼1 m·s (V1LOAD); and an incremental field test to determine maximal aerobic speed (MAS). U16 showed significantly (P = .000) greater gains for V1LOAD than U18 and U21 (100/0/0%). Only U16 showed significantly (P = .01) greater gains than U21 (99/1/0%) for CMJ height. U18 obtained a likely better effect on CMJ performance than U21 (89/10/1%). The beneficial effects on T20 between groups were unclear. U16 showed a likely better effect on MAS than U21 (80/17/3%), whereas the rest of comparisons were unclear. The changes in CMJ correlated to the changes in T20 (r = -.49) and V1LOAD (r = .40). In conclusion, velocity-based RT with moderate load and few repetitions per set seems to be an adequate methodology to improve the physical performance in young soccer players.