We compared the effects of two resistance training (RT) programs only differing in the repetition velocity loss allowed in each set: 20% (VL20) vs 40% (VL40) on muscle structural and functional adaptations. Twenty-two young males were randomly assigned to a VL20 (n = 12) or VL40 (n = 10) group. Subjects followed an 8-week velocity-based RT program using the squat exercise while monitoring repetition velocity. Pre- and post-training assessments included: magnetic resonance imaging, vastus lateralis biopsies for muscle cross-sectional area (CSA) and fiber type analyses, one-repetition maximum strength and full load-velocity squat profile, countermovement jump (CMJ), and 20-m sprint running. VL20 resulted in similar squat strength gains than VL40 and greater improvements in CMJ (9.5% vs 3.5%, P < 0.05), despite VL20 performing 40% fewer repetitions. Although both groups increased mean fiber CSA and whole quadriceps muscle volume, VL40 training elicited a greater hypertrophy of vastus lateralis and intermedius than VL20. Training resulted in a reduction of myosin heavy chain IIX percentage in VL40, whereas it was preserved in VL20. In conclusion, the progressive accumulation of muscle fatigue as indicated by a more pronounced repetition velocity loss appears as an important variable in the configuration of the resistance exercise stimulus as it influences functional and structural neuromuscular adaptations.