Objective: The purpose of this study was to investigate the effects of repeated sprint interval training (RSIT) under different hypoxic conditions in comparison with normoxic RSIT on cardiorespiratory fitness (CRF) and metabolic health in sedentary young women. Methods: Sixty-two sedentary young women (age: 21.9 ± 2.8 years, peak oxygen uptake [V̇O] 25.9 ± 4.5 ml kg·min) were randomized into one of the four groups, including a normoxic RSIT group (N), RSIT simulating an altitude of 2500 m (H), RSIT simulating an incremental altitude of 2500–3400 m (H) and a non-exercise control group (C). The training intervention (80 × 6 s all-out cycling sprints with 9 s recovery) was performed three times/week for 4 weeks. Anthropometric measures, V̇O, fasting blood glucose and lipids were assessed during the follicular phase of the menstrual cycle before and after the intervention. Results: Compared with the control group, significant increases in V̇O were found in both hypoxic groups (H: +8.2%, p < 0.001, d = 0.52; H: +10.9%, p < 0.05, d = 0.99) but not in the N group (+3.6%, p > 0.05, d = 0.21) after the intervention, whereas the two hypoxic groups had no difference in V̇O. Blood glucose and lipids, and body composition remained unchanged in all groups. Conclusion: The present study indicates that combining hypoxia with RSIT can enhance the improvement of CRF compared with normoxic RSIT alone in the sedentary young population. Yet, compared with RSIT under stable hypoxia, incremental hypoxia stress in the short-term does not additionally ameliorate CRF.