Background: Although mat Pilates (MP) has become popular, the effects of MP in hypertensive women (HW) are not entirely clear. Here, we investigated the effects of 16 weeks of MP training contrasted with MP supplemented with aerobic exercise (MP+AE) and compared with a non-intervention group on autonomic modulation, cardiorespiratory fitness, strength, flexibility, performance of functional tasks, QOL, anthropometric variables, clinical BP, and heart rate. Methods: This is a three-arm, secondary analysis of an RCT. Sixty HW, aged 30 to 59 years, were allocated into: MP only (MP), MP+AE on a treadmill (MP+AE), and Control Group, without exercises. Assessments were performed before and after 16 weeks of training. Results: The ANOVA shows differences in between-group comparisons in the SDNN, rMSSD, and SD1 in the heart rate variability analysis, with increases in rMSSD, SDNN, and SD1 only in the MP, and this result was not found in the MP+AE group (p < 0.05). Differences were observed in the between-group comparisons in time in the cardiorespiratory exercise test (CPX), flexibility, and the waist-to-hip ratio, with changes in the MP+AE, differences in QOL, and increments in the MP and MP+AE (p < 0.05). Conclusions: MP increased the indices that reflect vagal and global cardiac autonomic modulation. MP+AE improved the CPX performance, flexibility, QOL, and anthropometric variables. These results suggest that MP supplemented or not with AE has promising effects in HW.