Objective This systematic review aimed to assess the safety and effectiveness of acute intermittent hypoxia to improve motor outcomes in individuals with incomplete spinal cord injury. Data source Pubmed, Embase, Scopus, and Cochrane Library databases were searched. Review methods We only included randomized controlled trials (published up to September 2025) that met the following criteria: participants were adults with incomplete spinal cord injury; the intervention involved acute intermittent hypoxia with or without motor training; the control group received sham acute intermittent hypoxia with or without motor training; outcomes included motor functions. Risk of bias was evaluated using RoB2 tool. Risk and mean differences were computed, with a random-effects model. Results Nine randomized controlled trials ( n = 114) were included. Overall risk of bias was with some concerns. The review indicates that acute intermittent hypoxia is safe and has good treatment adherence, with low drop-out rates for acute intermittent hypoxia alone (RD = 0.08; 95% confidence interval (CI): −0.11–0.26; I 2 = 0%; n = 66) or with gait training (RD = 0.04; 95% CI: −0.11–0.18; I 2 = 0%; n = 57). Acute intermittent hypoxia was found to have beneficial effects on walking speed (MD = 5.97; 95% CI: 1.4–10.54; I 2 = 0%; n = 53), endurance (MD = 39.39; 95% CI: 1.92–76.86; I 2 = 50%; n = 54), muscle strength, and manual dexterity. However, no significant effects were observed on balance functions. Conclusion Acute intermittent hypoxia may be a promising adjunctive therapy to enhance motor function in individuals with incomplete spinal cord injury. Further research with standardized protocols and larger sample sizes is needed to optimize its use in clinical practice.