Polycystic Ovarian Syndrome (PCOS) is the most common endocrinopathy and cause of oligomenorrhea in women. The present study was conducted with the aim to compare the effect of Agnugol and Metformin drugs on oligomenorrhea in patients with PCOS. This study was a clinical trial on 120 women with PCOS and had oligomenorrhea, referring to a gynaecology clinic Fatemieh, Hamadan city, Iran, 2015. Women were randomly divided into 2 groups using permutation blocks (getting the medications Agnugol and Metformin) and were treated with drugs Agnugol and Metformin for 3 months. Data collection included demographic questionnaire and check list was designed and completed before and at the end of interventions, by both groups. To analyse the data, descriptive statistics, chi-square tests, t-test, ANOVA with repeated measures was used. The mean and SD of age was 39.45±4.60 for women taking Agnugol and 38.466±0.84 for those taking Metformin. Based on the results between the subjects, the two groups were not significantly different in terms of menstruation length, cycle intervals, or the number of pads, meaning that the two drugs had similar effects on menstrual cycle regulation, menstruation length and the number of pads. More side effects were reported in the group using Metformin. Agnugol and Metformin drugs in the treatment of oligomenorrhea patients with PCOS have the same effect. Since Metformin is a chemical drug with side effects, Agnugol can be presented as its herbal alternative to treat oligomenorrhea.