Polycystic ovary syndrome (PCOS) is one of the most common endocrine disorders in women of reproductive ages. The purpose of this study was to determine the effect of eight weeks endurance training on ovarian hormones in PCOS women with use of application of multivariate longitudinal models. In order to 40 PCOS women (age: 16-40 years) in Isfahan city were selected by convenience sampling and randomly divided into two groups of intervention (n= 20) and control (n= 20). Subjects of intervention group performed endurance training included running with a severity of 60 to 75% of maximum heart rate for 8 weeks, 3 sessions per week, each session 20-30 minutes. Blood samples were collected before of first session training and 48 hours after the last training session, after at least 10 hours of fasting in days 2 to 4 menstruation according to the menstrual period. The ELISA method was used to measure the testosterone, prolactin, LH and FSH variables. With respect to association between these biomarkers, multivariate longitudinal modeling approach was used with R 3.4. 1 software at a significant level of 0.05. Results showed a significant effect of the intervention on LH and prolactin variables (P< 0.001), but aerobic exercise did not show a significant effect on testosterone and FSH. Also, the highest effect of exercise on prolactin hormone (effect size= 0.39) and the lowest effect on FSH (effect size= 0.02). Eight weeks of regular aerobic exercise, while affecting ovarian androgens in PCOS women, can be considered as a safe treatment for these patients.