BACKGROUND: Polycystic ovary syndrome (PCOS) is one of the most frequent endocrine disorders among women of fertile age. Women with PCOS manifest clinical symptoms like menstrual dysfunction, hirsutism, insulin resistance, and hyperinsulinemia. As excessive amounts of insulin levels directly increase ovarian production of androgens, hyperinsulinemia and insulin resistance are considered as the pathogenesis factors of PCOS. The portfolio low-carbohydrate diet (PLCD) is a plant-based diet with 40% carbohydrates combined with five cholesterol-lowering foods and nutrients. On the other hand, the ketogenic diet (KD) is a nutritional protocol with 10% carbohydrates. The purpose of this study is to determine whether PLCD or KD is more effective in alleviating PCOS symptoms. METHODS: Forty-six overweight or obese women diagnosed with PCOS will be randomly stratified to receive either PLCD or KD for 8 weeks. Measures related to anthropometric and body composition, glucose, and insulin level, HOMA-IR, sex hormones, lipid profile, quality of life, dietary intake, physical activity, and Ferriman-Gallwey score of all participants will be accessed before and after the intervention. DISCUSSION: Since the first line treatment of PCOS is lifestyle adjustment including diet control and exercise, there has not been determined the optimal diet for this population of women yet. Hence, the goal of conducting this study is to determine whether the PLCD or the KD could have more advantageous effects on attenuating PCOS manifestations. The result of this investigation will give us new insight into curing this disease and will provide evidence-based recommendations for prescribing an optimal diet for PCOS women. TRIAL REGISTRATION: IRCT20200912048693N3, Trial registered 2022-12-14. https://www.irct.ir/trial/67548.