To investigate relationships between weight loss and weight loss maintenance with cardiac autonomic function and exercise in obesity, 39 adults (45.7±10.7 years; BMI: 34.2±3.4 kg/m2) participated in a 10-week, medical weight loss program combined with aerobic exercise. A subset (n=18) participated in an aerobic exercise weight loss maintenance program (550 or 970 MET minutes/week) for 18 additional weeks. Primary outcomes included markers of cardiac autonomic function assessed by heart rate variability (HRV) (i.e., SDNN, RMSSD, HFln). Following weight loss, we observed significant improvements for SDNN (48.2±19.1 vs. 55.1±25.9 ms, p=0.03) RMSSD (37.7±24.0 vs. 47.9±29.1 ms, p=0.002), and HFln (5.88±1.34 vs. 6.32±1.28 ms, p=0.001). Regression analyses showed fasting insulin concentration predicted 24% and 27% of the variance in RMSSD (r2=0.236, p=0.007) and HFln (r2=0.274, p=0.004), respectively. Following weight loss maintenance, no significant changes in HRV were observed. Changes in LDL (r=–0.54, p=0.04) and non-HDL (r=–0.77, p=0.001) were inversely associated with RMSSD changes. Clinically significant weight loss via caloric restriction and aerobic exercise improved HRV markers of cardiac vagal modulation. Following weight loss maintenance, we did not observe any further changes in HRV. Thus, our data suggests commonly prescribed exercise volumes contribute to maintenance of parasympathetic modulation following medical weight loss programming and exercise.