High-intensity interval training (HIIT), is effective to improve cardiorespiratory fitness (CRF) and metabolic syndrome (MetS) components in adults. However, it is unclear if CRF and MetS components respond similarly in men and women after HIIT. For 16 weeks, 63 women (53±7 years) and 56 men (55±8 years) with MetS underwent a three day/week HIIT program. Bodyweight and composition, VO2MAX, surrogate parameters of CRF (Ventilatory threshold (VT), oxygen uptake efficiency slope (OUES) and VE/VCO2 slope), maximal rate of fat oxidation (MFO), and MetS components were assessed before and after training. All reported variables were analyzed by split-plot ANOVA looking for time by sex interactions. Before training men had higher absolute values of VO2MAX (58.6%), and MFO (24.6%), while lower body fat mass (10.5%) than women (all P<0.05). After normalization by fat-free mass (FFM), VO2MAX remained 16.6% higher in men (P<0.05), whereas differences in MFO disappeared (P = 0.292). After intervention VO2MAX (P<0.001), VO2 at VT (P<0.001), OUES (P<0.001), and VE/VCO2 slope (P<0.001) increased without differences by sex (P>0.05). After training MetS Z-score (P<0.001) improved without differences between men and women (P>0.05). From the MetS components, only blood pressure (P<0.001) and waist circumference (P<0.001) improved across time, without differences by sex. In both, women and men, changes in OUES (r = 0.685 and r = 0.445, respectively), and VO2 at VT (r = 0.378, and r = 0.445, respectively), correlated with VO2MAX. While only bodyweight changes correlated with MetS Z-score changes (r = 0.372, and = 0.300, respectively). Despite baseline differences, 16-weeks of HIIT similarly improved MetS, cardiorespiratory and metabolic fitness in women and men with MetS. This suggests that there are no restrictions due to sex on the benefits derived from an intense exercise program in the health of MetS participants. Trial Registration: clinicaltrials.gov NCT03019796.