Polycystic ovary syndrome (PCOS) is associated with menstrual disorders and hyperandrogenism, which is considered to be a common cause of hirsutism and infertility. Chamomile has been used as a medicinal herb known for its menstrual property. This study aimed to investigate the effect of chamomile on the menstruation pattern and serum androgens in PCOS women. This study was a randomized clinical trial, conducted on 80 women during their reproductive age with PCOS from April 2014 to August 2015. They were divided into intervention and control groups. The intervention group received a chamomile capsule (containing 370 mg dried powder of German chamomile flower) three times a day for 12 weeks, while the control group received placebo (starch-based capsules) with the same prescription order. Menstrual questionnaires as well as the androgens of testosterone and dehydroepiandrosterone were examined before and after 3 months. The primary outcome in the chamomile capsules user group, the number of participants with normal menstrual cycles significantly increased (p<0.001). In addition, a significant improvement in the number of menstrual cycles after the chamomile therapy was observed. A significant decrease was observed in testosterone levels in the intervention group. However, there was no significant change in the level of hormone dehydroepiandrosterone sulfate in both intervention and control groups (P = 0.423). Chamomile can have a significant impact on menstrual regulation and decrease the total testosterone levels in women of reproductive age with polycystic ovary syndrome. It is recommended that careful, large randomized controlled trials should be conducted to understand the mechanisms of action of chamomile and its effects on menstruation process.