This study examined the impact of weekly eccentric overload training (EOT) on locomotor and mechanical performance during small-sided games (SSGs) in elite youth soccer players. A total of 22 elite male youth soccer players participated in this study. A controlled, non-randomized study design was employed. Players were assigned to either an eccentric overload training group (EOT, n = 9) or a control group (CON, n = 13). The EOT group incorporated one additional eccentric training session into their regular regimen, while the control group maintained their standard training schedule throughout the 8-week study. The Eccentric Overload Training (EOT), known for its benefits in injury prevention and performance enhancement, incorporated five exercises using flywheel devices: K-box squats, split squats, dynamic forward and backward lunges, and unilateral hamstring kicks on the Versa-Pulley. A total of 1,117 small-sided game (SSG) observations were analyzed (EOT = 528, CON = 589). No significant differences were found in locomotor variables, including zScore for total distance covered (TD), high-speed distance (HSD), very high-speed distance (VHSD), and sprint distance (SD). However, the intervention group showed lower acceleration (ACC) and deceleration (DEC) compared to controls (p < 0.05). Player load (PL) varied significantly between groups and over time (p < 0.05). These findings suggest that incorporating a weekly eccentric overload training (EOT) session may enhance locomotor performance despite temporary reductions in mechanical performance in elite youth soccer players. The practical application of the study is that minimal preventive eccentric work can be added into the intervention process without compromising physical performance capacity during that period.