During the COVID-19 pandemic, people are concerned about wearing a mask during physical activity and its effect on the cardiac autonomic system (ANS). The purpose of the study was the effect of 2-weeks of moderate-intensity interval training (MIIT) based body weight combined with wearing face masks (surgery against N95) on the ANS response of healthy men following the submaximal treadmill running protocol (STRP) and 5 minutes of recovery during the SARS-CoV-2 pandemic. This study,18 healthy men were randomly divided into 3 groups of 6 (surgical mask,N95 mask and Nomask) and MIIT exercises with and without surgical masks or N95 3-times a week, each session with 3-repetitions with intensity (60-70% Maximum-heart rate). Parasympathetic (RMSSD, HFn.u) and sympathetic parameters (LFn.u, LF/HF) and Change distance R-R were evaluated with electrocardiogram and Kubius software before and to 5 minutes of recovery. One-way ANOVA and Bonferroni post hoc test were used. The results showed, STRP protocol Implementation before 2-weeks of MIIT did not make a significant difference in LF, LF/HF, RMSSD, HF and mean RR values between the experimental groups (surgical mask against N95 mask) and also compared with the control group (without mask(. In addition, although the intergroup changes in sympathetic and parasympathetic indices and mean RR after 2-weeks of MIIT show relative improvement, they have not yet been statistically significant. Wearing facemasks during exercise training is safe for healthy men and 2 weeks of adaptation to interval training with face mask improves ANS performance.