Obesity and type 2 diabetes (T2D) are associated with abnormal cardiovascular autonomic function and increased risk for cardiac complications, especially after exercise. Since improvements at rest are not always observed after training, we investigated changes in resting and post-exercise autonomic function in obese women with and without T2D after16-week of walking training. Heart rate (HR) variability (HRV) and baroreflex sensitivity (BRS) were measured at rest and 20 min after a 20 min bout of treadmill exercise at 65% VO₂ peak in obese women with (n = 8) and without T2D (n = 12) before and after training. HRV was analyzed by frequency-domain [high- (HF) power and low-frequency (LF)] and BRS by the sequence method. Exercise training induced similar significant changes in VO₂ peak, resting systolic blood pressure (SBP) and post-exercise autonomic function in both groups. Training increased VO₂ peak (6%; P < 0.01) and decreased resting SBP (8%; P < 0.001). Increased post-exercise HR recovery (5%; P < 0.001), HF power (14%; P < 0.05), LF power (14%; P < 0.05) and BRS (86%; P < 0.001) were also observed. Resting autonomic function and post-exercise SBP were not altered after training. In conclusion, endurance training reduced blood pressure without changes in HRV and BRS at rest, but training increased HRV and BRS during the recovery of acute endurance exercise indicating an improved post-exercise autonomic modulation of HR, which was similar in obese women with and without T2D.