Purpose Systemic hypoxia (SH) and blood flow restriction (BFR) are methods used to improve repeated sprint exercise ability. This study aimed to compare their respective impacts on neuromuscular fatigue etiology of the lower limbs during cycling sprints, using an innovative instrumented cycle-ergometer allowing immediate measurements between sprints. Method Fifteen participants performed repeated 10-s cycling sprints/28-s recovery until a 30% decrease in sprint mean power, under two randomized conditions: BFR (45% arterial occlusion) and SH (FiO2 = 0.13). Isometric maximum voluntary contraction of the quadriceps (IMVC), muscle pain, and central (voluntary activation, VA) and peripheral (peak twitch, Pt) alterations were evaluated before and immediately after each sprint. Peripheral oxygen saturation (SpO2, pulse oximetry) and quadriceps muscle oxygenation (TSI, near-infrared spectroscopy) were continuously recorded. Results Participants completed 8.3 ± 4.3 sprints with BFR and 7.3 ± 3.0 sprints in SH, with no difference between conditions and similar initial mean power. Pt was similarly affected in both conditions, but IMVC and VA decreases were exacerbated in BFR (VA pre-post −20 ± 14% vs. −7 ± 9% in SH, p textless 0.001). Muscle pain was higher in BFR compared to SH (87 ± 18 vs 76 ± 20, respectively, p = 0.02). Sprint-induced muscle deoxygenations were similar in BFR and SH conditions. Conclusions Sprint performance and localized hypoxia were similar between conditions, but neuromuscular fatigue was exacerbated in BFR compared to SH, primarily driven by enhanced central drive impairments along with elevated quadriceps pain perception. Practically, although BFR and SH produce comparable mechanical performance decrements, BFR imposes a substantially greater central and perceptual load that practitioners should consider when designing repeated-sprint training interventions.