Background: The effects of flywheel resistance training (FRT) on youth are relatively unknown. The aim of this study was to compare the effects of autoregulated FRT with traditional strength training (TST) on jumping, running performance and resistance training load progression in youth athletes. Thirty youth athletes (11.8 ± 0.9 yr) were matched for peak height velocity (PHV) status and block-randomised into two groups: FRT (n = 15, PHV −0.8 ± 1.6) and TST (n = 15, PHV −0.8 ± 1.5). Twelve resistance training sessions over a six-week intervention with flywheel or barbell squats were performed using autoregulated load prescription. Squat jump (SJ); countermovement jump (CMJ); and 10 m, 20 m and 30 m sprints were assessed pre- and post-intervention. The external load increased similarly for FRT and TST (z = 3.8, p = 0.06). SJ increased for both groups (p < 0.05) but running performance was unaffected (p > 0.05). Conclusions: FRT resulted in similar load progression and motor skill development in youth athletes as TST, but the perceived exertion was less. Autoregulation is a practical method for adjusting training load during FRT and should be considered as an alternative to autoregulated TST.