The present study aimed to determine the effects of 12 weeks of aerobic exercise in different times of day on some cardiovascular risk factors in overweight men. 40 non-athletes, overweight men with an average age of 22.25±2.45 years old and BMI of 30.06±2.42 kg/m2 were randomly allocated to four groups of morning and evening aerobic training and control. Morning and evening training groups performed the aerobic training protocol three sessions per week for 12 weeks with 75 to 85 percent of maximal heart rate and 15 minutes training per session. The training time was increasingly added 1.5 minutes every three sessions until the training time reached 30 minutes. The control groups were instructed not to do the training program during the research period. Blood samples (5 cc) were taken from the participants at the beginning of the research period, week 6 and the end of week 12 in order to measure cardiovascular risk factors (i.e. triglyceride, low density lipoprotein, high density lipoprotein and cholesterol). The obtained data were analyzed using analysis of variance (ANOVA) and t-test with the Bonferroni correction for within-group evaluation and one-way analysis of variance along with Toki post-hoc test for between-group evaluation (α<%5). The results showed that morning and evening aerobic training significantly decreased LDL-c and significantly increased HDL-c in the experimental groups compared to the control groups. However, the total levels of cholesterol and triglyceride remained unchanged in these groups. In addition, no significant difference was observed in LDL-c and HDL-c levels between morning and evening training groups when the training was completed. It was also demonstrated that aerobic training during morning and evening could influence the compatibility of cardiovascular risk factors. And finally, no difference between the effect of aerobic exercise during morning and evening was observed on overweight men.