Post-exercise heart rate recovery (HRR) has been proposed as a measure of cardiac autonomic dysfunction in apparently healthy adults. We aimed to determine the effects of a lifestyle intervention on HRR among clinically obese premenopausal women. A randomized controlled trial was conducted to investigate the effects of a 3-month non-dieting lifestyle intervention program on cardiorespiratory fitness (CRF) and HRR among healthy clinically obese premenopausal women. Thirty-one were randomly assigned to 3-month intensive lifestyle intervention and 31 served as controls. Sixty-one participants performed a maximal treadmill walking test with metabolic gas exchange. Baseline anthropometric measures were closely related to HRR at 1 min, which may indicate reduced parasympathetic reactivation. Post-exercise HRR at 60 s (HRR60) increased from 21.3 ± 6.2 to 27.8 ± 10.2 bpm in the intervention group compared with a smaller reduction (26.8 ± 12.3 to 24.5 ± 9.9 bpm) in controls (test for interaction P = 0.0001). HRR120 showed a significant effect of time (P = 0.0002) with no significant interaction with lifestyle intervention. A significant increase in was evident in the lifestyle group (21.6 to 23.6 mL/kg/min) compared with a modest reduction in the controls (22.6 to 21.6 mL/kg/min; test for interaction, P = 0.001). Clinically obese healthy premenopausal women achieved significant improvements in HRR60 and following a 3-month intensive lifestyle intervention.