Intervention programs to prevent or treat Burnout Syndrome are essential to improve the health of students. But most of the research that has been done is psychological and cognitive interventions. Objective: To determine the effects of physical exercises on Burnout Syndrome levels and Heart Rate Variability in university students. Methods: An experimental study was carried out with pre-test and post-test, with 2 intervention groups and a control group. The sample was probabilistic and stratified with proportional participation. Study variables and instruments were included: Maslach Burnout Inventory Students Survey (MBI-SS) and Heart Rate Variability (HRV): calculation of the average RR, SDNN and RMSSD. For physical exercise, aerobic and strength exercises were applied during 3 weekly sessions of one hour, on alternate days, for 16 weeks. Results: The group of aerobics with MBI-SS exhaustion was higher, reducing its levels by 26.4% (d=0.532), in Cynicism (-21.06, d=0.252) and Efficiency (-13.11, 0.397). Force group in Cynicism (-27.38, d=0.315), in Efficiency (-21.69, d=0.704), Exhaustion (-19.55, d=0.299). The Exhaustion control group increased by 10.26% (d=0.128). In HVR, with the aerobic group, NDL had the greatest percentage change, increasing 24,82 %, over the average RR and RMSSD (14,40 % and 16,45 %). In the force group and in the control group (21.77%, 14.24%, 12.60%; and 12.59%, 4.97% and 4.99% respectively) there was a change in the mean RR in the aerobic and strength groups (d = 1.281 and 1.328). Conclusions: Effect of reduction of burnout syndrome and opposite effect of increase of HRV values.