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The purpose of this study was to investigate the effect of plyometric training on running velocity (RV) and squat jump (SJ) in prepubescent boys. Fifteen boys (11.1 ± 0.5 years) followed a 10-week plyometric program (JUMP group). Another group of 15 boys (10.9 ± 0.7 years) followed only the physical education program in primary school and was used as the control group (CONT group). Running distances (0–10 m, 10–20 m, 20–30 m, and 0–30 m), were selected as testing variables to evaluate the training program. The total number of jumps was initially 60 per session, which was gradually increased over a period of 10 weeks to 100 per session. Results revealed significant differences between CONT and JUMP groups in RV and SJ. In JUMP group the velocity for the running distances 0–30, 10–20, and 20–30 m increased (p < 0.05), but not for the distance 0–10 m (p > 0.05). Additionally, the SJ performance of the JUMP group increased significantly, as well (p < 0.05). There was no change in either RV or SJ for the CONT group. These results indicate that plyometric exercises can improve SJ and RV in prepubertal boys. More specifically, this program selectively influenced the maximum velocity phase, but not the acceleration phase.