Background and aim. — COVID-19 as a viral disease has brought up the need to exercise more than before due to its physiological effects on health. Therefore, this study investigates the effect of 12-week of aerobic exercise on female students’ hormone levels and lipid profile with polycystic ovary syndrome (PCOS) during the COVID-19 pandemic. Method. — Using a 12-week quasi-experimental with pretest, posttest research design among 40 Iranian female students aged 18—14 with PCOS, we randomly allocated the participants to either an experimental (they performed aerobic exercises three 60-minute sessions per week at home using content production) or a control condition. Their anthropometric and blood samples (e.g., testosterone, estrogen, prolactin, and lipid profile) were taken in two stages before and after the training protocol. Results. — The results of analysis indicated that 12-week of aerobic exercise reduced testosterone (P = 0.041), prolactin (P = 0.001), estrogen (P = 0.001), body mass (P = 0.002), body mass index (P = 0.002), cholesterol (P = 0.005), triglyceride (P = 0.001) and low-density lipoprotein (P = 0.001), whilst increased high-density lipoprotein (P = 0.002).Conclusion. — Findings demonstrated that performing aerobic exercises is an effective and non-invasive method that could have a positive effect on young girls’ PCOS during COVID-19 pandemic.