Cardiac autonomic neuropathy is a common complication of type 2 diabetes mellitus (T2DM), that can be measured through heart rate variability (HRV)-known to be decreased in T2DM. Physical exercise can improve HRV in healthy population, however results are under debate in T2DM. We conducted a systemic review and meta-analysis to assess the effects of physical exercise on HRV in T2DM patients. PubMed, Cochrane, Embase, and ScienceDirect databases were searched for all studies reporting HRV parameters in T2DM patients before and after exercise training, until September 20th 2020, without limitation to specific years. We conducted random-effects meta-analysis stratified by type of exercise for each of the HRV parameters: RR-intervals (or Normal to Normal intervals-NN), standard deviation of RR intervals (SDNN), percentage of adjacent NN intervals varying by more than 50 milliseconds (pNN50), root mean square of successive RR-intervals differences (RMSSD), total power, Low Frequency (LF), High Frequency (HF) and LF/HF ratio. Sensitivity analyses were computed on studies with the highest quality. We included 21 studies (9 were randomized) for a total of 523 T2DM patients: 472 had an exercise training and 151 were controls (no exercise). Intervention was endurance (14 studies), resistance (2 studies), endurance combined with resistance (4 studies), and high intensity interval training (HIIT) (4 studies). After exercise training, all HRV parameters improved i.e. an increase in SDNN (effect size = 0.59, 95%CI 0.26 to 0.93), RMSSD (0.62, 0.28 to 0.95), pNN50 (0.62, 0.23 to 1.00), HF (0.58, -0.16 to 0.99), and a decrease in LF (-0.37, -0.69 to -0.05) and LF/HF (-0.52, -0.79 to -0.24). There were no changes in controls. Stratification by type of exercise showed an improvement in most HRV parameters (SDNN, RMSSD, pNN50, LF, HF, LF/HF) after endurance training, whereas mostly LF/HF was improved after both resistance training and HIIT. Supervised training improved most HRV parameters. Duration and frequency of training did not influence the benefits on HRV. Exercise training improved HRV parameters in T2DM patients which may reflect an improvement in the activity of the autonomic nervous system. The level of proof is the highest for endurance training. Supervised training seemed beneficial.