The purpose of this study was to examine the effects of a 6-month high- or moderate-intensity total-body circuit training (CT) program on physical fitness in prepubertal soccer players. Sixty-seven prepubertal boys with a mean age of 11.2 ± 0.7 years completed the study. Participants from a soccer academy were randomly assigned either to a high-intensity CT group (HCT, n = 22) or a moderate-intensity CT group (MCT, n = 24). A control group (CON, n = 21) comprised age-matched individuals who were not involved in any regular training regime. CT protocols were included in the experimental group's training sessions 3 times per week over 24 weeks as part of their usual weekly training regime. Based on the HR zone method, CT protocols included high- or moderate-intensity (85-95% HR or 75-85% HR) series of 3 different sets of upper- and lower-body strength exercises with articular and muscular mobilization, all culminated with 40-m sprints. Physical fitness was evaluated by the Eurofit test which included the flamingo balance (FLB), plate tapping (PLT), sit-and-reach (SAR), standing broad jump (SBJ), handgrip (HG), sit-ups (SUP), bent arm hang (BAH), 10×5 m shuttle run (SHR), and the Physical Working Capacity test (PWC). The two-way ANOVA indicated group×time interaction effects for 5 components: the largest was for the SBJ (F = 42.895, p < 0.001, η = 0.577), and the lowest for the SHR (F = 5.006, p < 0.01, η = 0.137) indicating better improvements in the HCT compared to the MCT group. Furthermore, for HCT and MCT groups the highest pre- to post-intervention percentage changes were for the FLB and the SAR, while in the CON group the changes of all physical fitness components were not significant (p < 0.05). In conclusion, the intensity-controlled total-body CT protocol incorporated into a standard soccer training program is effective for enhancement in physical fitness performance in prepubertal soccer players.