Purpose: To compare the effects of velocity-based training (VBT) vs percentage-based training (PBT) on strength, speed, and jump performance in academy rugby league players during a 7-wk in-season mesocycle. Methods: A total of 27 rugby league players competing in the Super League U19s Championship were randomized to VBT (n = 12) or PBT (n = 15). Both groups completed a 7-wk resistance-training intervention (2×/wk) that involved the back squat. The PBT group used a fixed load based on a percentage of 1-repetition maximum (1-RM), whereas the VBT group used a modifiable load based on individualized velocity thresholds. Biomechanical and perceptual data were collected during each training session. Back-squat 1-RM, countermovement jump, reactive strength index, sprint times, and back-squat velocity at 40–90% 1-RM were assessed pretraining and posttraining. Results: The PBT group showed likely to most likely improvements in 1-RM strength and reactive strength index, whereas the VBT group showed likely to very likely improvements in 1-RM strength, countermovement jump height, and back-squat velocity at 40% and 60% 1-RM. Sessional velocity and power were most likely greater during VBT compared with PBT (standardized mean differences = 1.8–2.4), while time under tension and perceptual training stress were likely lower (standardized mean differences = 0.49–0.66). The improvement in back-squat velocity at 60% 1-RM was likely greater following VBT compared with PBT (standardized mean difference = 0.50). Conclusion: VBT can be implemented during the competitive season, instead of traditional PBT, to improve training stimuli, decrease training stress, and promote velocity-specific adaptations.