Abstract Sex differences in near-infrared spectroscopy (NIRS) reactive hyperemia outcomes have been previously reported, with females generally having a lower reperfusion slope. Sex differences have also been reported for adipose tissue thickness (ATT), which affects the NIRS signal, and desaturation during occlusion, which may act on reperfusion slopes. We aimed to compare statistically adjusted and unadjusted sex differences in reperfusion slope during reactive hyperemia. Methods 23 female and 22 male participants completed forearm and thigh vascular occlusion tests. ATT was measured via ultrasound. Reperfusion slopes (StO2%/s) were compared between sexes using linear models with and without desaturation slope (StO2%/s) and ATT as covariates. Results are mean or mean difference [95 % CI]. Results In both limbs, females had greater ATT (p textless 0.001). Desaturation rate was lower in females for the leg (−0.02 [−0.03, −0.01]), but not the arm (0.00 [−0.01, 0.02]). Unadjusted, males had greater reperfusion slope in the leg (females = 0.91 [0.70, 1.11], males = 1.59 [1.33, 1.85], p textless 0.001) but not the arm (females = 1.60 [1.36, 1.84], males = 1.57 [1.29, 1.86], p = 0.874). Sex differences were not observed in adjusted models (both p ≥ 0.631). ATT and desaturation slope explained unique variance in the leg (both p ≤ 0.001), but only desaturation slope did in the arm (p textless 0.001). Conclusion Sex differences may have been related to differing ATT and desaturation rates. Researchers may consider adjusting for ATT and/or desaturation rate when estimating sex differences with NIRS reactive hyperemia.