Background: Physical activity influence differently on health indices including premenstrual syndrome (PMS) which can be related to various exercise characteristics. The aim of Present study was to evaluate the effect of interval training with high and average intensity on PMS, body mass index (BMI) and cardiorespiratory fitness (CRF) in young collegiate female students. Materials and methods: Participants were 60 nonathletic healthy (physically and psychologically) female collegiate students. They were selected and randomly divided into two groups of high intensity (n=30) and moderate intensity (n=30) interval training. Rating and intensity of premenstrual symptoms (using Moos questionnaire), CRF (Using Copper test) and BMI of participants were measured before and after training program. Training program included warm up for 20 minutes, following 35 minutes high intensity interval running (maximum heart rate 80-90%) or moderate intensity running (maximum heart rate 50-60%) and cooling down for 5 minutes for 8 weeks, once every week. Exercise volume was assimilated in both groups. Data was analyzed using covariance statistical testing and t-test. Results: Comparison of high and moderate intensity training groups indicated that there was no significant difference in psychological (p=0.708) and physical (p=0.163) symptoms of PMS and CRF (p=0.183) following exercise training. But BMI was significantly lower in average compared to high intensity groups (p=0.003). Within group evaluations indicated that interval training with high and moderate intensity does not affect significantly physical and psychological symptoms of PMS but decreases BMI and increase CRF significantly. Conclusion: High and moderate intensity exercise training in general physical education course does not affect significantly PMS but improve BMI and CRF. Average intensity training is more effective in reducing BMI.