This study aimed to compare physiological responses to high-intensity interval exercise (HIIE) in hypoxia and normoxia across different body mass index (BMI) categories. Twenty-one males, classified as normal-weight (NW, n = 9 and BMI: 22.9 ± 2.3 kg · m) or overweight/obese (OW, n = 12 and BMI: 27.6 ± 2.0 kg · m), completed graded exercise tests (GXT) in normoxia (FiO = 20.9%) and hypoxia (FiO = 14.0%), followed by three randomised HIIE sessions: hypoxia (HY), normoxia matched to hypoxic relative intensity (NR) and normoxia matched to hypoxic absolute intensity (NA). Blood samples were collected at baseline, immediately post-HIIE and at 3 and 24 h post-exercise. Both NW and OW groups had significant reductions in peak heart rate and peak power output in hypoxic versus normoxic GXT (p < 0.05). The NW group showed a greater decline in peak oxygen uptake under hypoxia compared to OW (Δ = 9.88 ± 5.0 vs. 5.22 ± 3.3 mL · kg · min; p < 0.001). OW exhibited increased blood glucose levels post-hypoxic GXT compared to normoxic conditions (Δ = 0.358 mmol · L; p = 0.025). During HIIE sessions, both groups showed similar heart rate, oxygen consumption, carbon dioxide production and respiratory exchange ratio responses. However, blood lactate concentration immediately after normoxic HIIE (NR) was higher in NW compared to OW (p < 0.05). Fasting blood glucose significantly increased immediately after normoxic HIIE in NW and immediately after hypoxic HIIE in OW (p < 0.05). HIIE in normoxia and hypoxia elicits similar physiological responses across BMI categories, though normal-weight individuals have greater reductions in and higher lactate responses during normoxic HIIE (NR), whereas overweight/obese individuals exhibit higher glucose increases post-hypoxic exercise, indicating potential BMI-specific metabolic benefits. These findings suggest that BMI could influence physiological adaptations in response to high-intensity exercise in hypoxia, suggesting that this form of exercise could be a beneficial alternative for improving metabolic health, especially in individuals with overweight or obesity.