Purpose To investigate the effect of aerobic exercise (AE) versus resistance exercise (RE) on outcomes of cardiac autonomic recovery in type 2 diabetes mellitus (T2DM) patients with cardiac autonomic neuropathy (CAN). Methods Fifty T2DM patients with CAN (age: 52.2 ± 6.8 years) were recruited for the present study. They were randomly allocated into two groups: AE (n = 25) and RE (n = 25). The AE group performed graded maximal exercise test using Balke protocol while the RE group performed 5 sets of leg press exercise at 10 repetition maximum (RM) intensity. Heart rate variability (HRV) was assessed for 10 min after both exercise bouts while heart rate recovery (HRR) was recorded for the first 3 min after completion of the exercise bouts. Key outcome measures for the study were standard time and frequency domain parameters of HRV and HRR 1min , HRR 2min , and HRR 3min . Standard statistical analysis which included independent t-test and repeated measures analysis of variance was performed in order to test the study hypothesis. Results Significant impairment was observed in both HRV and HRR after both AE and RE (p < 0.05). However, alterations in both HRV and HRR responses were found to be more after AE as compared to RE (p < 0.05) in T2DM patients with CAN. Conclusion Findings of the present study suggest significant blunting of autonomic responses after both AE and RE in T2DM patients with CAN. However, deterioration in them was found to be more after AE as compared to the RE indicating that AE may pose greater stress on the cardiovascular system of T2DM patients with CAN.