This randomized clinical trial aimed to examine the effects of a 6-month home-based, combined exercise training program on Cardiac Autonomic Neuropathy (CAN) in kidney transplant recipients (KTRs) with diabetes. Twenty-five KTRs (19 men (76.0%), with a mean age of 54.4 ± 11.3 years old, CAN and type II Diabetes Mellitus (DM-II)), were randomly assigned into two groups: A (n1= 13 KTRs), who underwent a home-based exercise training program for 6 months, and B (n2= 12 KTRs), who were assessed at the end of the study. A cardiopulmonary exercise testing (CPET), sit-to-stand test in 30 s (30-s STS), isokinetic muscle strength dynamometry, and 24-h electrocardiographic monitoring were applied to all participants, both at the baseline and at the end of the clinical trial. At first, there were no statistically significant differences between groups. After 6 months, group A showed higher values in exercise time by 8.7% (p= 0.02), VO2peak by 7.3% (p< 0.05), 30-s STS by 12.0% (p< 0.05), upper limb strength by 46.1% (p< 0.05), and lower limb strength by 24.6% (p= 0.02), respectively, compared to the B group. Furthermore, inter-group changes at the end of the 6-month study indicated that group A statistically increased the standard deviation of R-R intervals (SDNN) by 30.3% (p= 0.01), root mean square of successive differences between normal heartbeats (rMSSD) by 32.0% (p= 0.03), number of pairs of successive NN (R-R) intervals that differ by more than 50 ms (pNN50) by 29.0% (p= 0.04), high frequency (HF (ms2)) by 21.6% (p< 0.05), HF (n.u.) by 48.5% (p= 0.01), and turbulence slope (TS) by 22.5% (p= 0.02), and decreased the low frequency (LF (ms2)) by 13.2% (p= 0.01), LF (n.u.) by 24.9% (p= 0.04), and LF/HF ratio by 24% (p= 0.01), compared to group B. Linear regression analysis after the 6-month study showed that there was a strong positive correlation between VO2peak and SDNN (r = 0.701,p< 0.05) in group A. Moreover, multiple regression analysis showed that KTRs’ participation in the exercise program showed favorable modifications to sympathovagal balance and aerobic capacity, as measured with SDNN and VO2peak, respectively. To summarize, diabetic KTRs’ cardiac autonomic function and functional capacity can be improved after a home-based long-term exercise training program.