Introduction. Many patients who were diagnosed as polycystic ovary syndrome- (PCOS-) related acne were not capable of sustaining or beginning oral contraceptive pills (OCPs) due to pill scaring, contraindications of OCP use, migraine, or smoking. In this situation, oral isotretinoin treatment may become an important option for PCOS-related acne. The aim of the study was to determine the effects of isotretinoin treatment on PCOS patients who were complicated with severe cystic acne. Materials and Methods. This study consisted of 40 female patients diagnosed as PCOS complicated with severe cystic acne. These patients were not eligible candidates for OCP use due to migraine, thrombophilia, heavy smoking, or pill scare. To establish baseline values of hormone levels, on days 2–5 of the menstrual cycle, venous blood samples were obtained. Moreover Modified Ferriman-Gallwey (mFG) score, acne score (AS), follicle count, and bilateral ovarian volumes were evaluated both before and after isotretinoin treatment. Results. Isotretinoin treatment significantly decreased Ferriman-Gallwey score, free testosterone, insulin level, hemoglobin level, acne score, and ovarian volume. Increased triglyceride and cholesterol levels were detected after treatment. Conclusion. Isotretinoin treatment may have beneficial effects on free testosterone, insulin, acne score, and Ferriman-Gallwey score. Solely isotretinoin administration may supply adequate healing in PCOS patients’ symptoms complicated with severe cystic acne who is not eligible candidates for OCP use. This trial is registered with Clinicaltrials.gov NCT02855138.