Obesity increases the detrimental effects on both reproductive and metabolic indicators of polycystic ovarian syndrome (PCOS). The ketogenic diet affects the outcomes of reproductive and metabolic characteristics in PCOS women. Adipose tissue is recognized as a novel gland by releasing diverse peptides called adipokines, like betatrophin, endorphin, and meteorite-like proteins. Although the ketogenic diet's impact on many adipokines in various diseases was examined, its effects on the adipokines level in PCOS have not yet been studied. Therefore, our paper attempts to investigate how the ketogenic diet affects the adipokines level in obese PCOS women. Because seventy obese women with PCOS did not follow our randomized clinical trial design, they were excluded, and only 50 obese women with PCOS completed and concluded the study. Adipokines (betatrophin, endotrophin, and meteorin-like protein) level was measured for all obese PCOS before and after adhering to 3 and 6 months of the ketogenic diet. From the baseline (before adhering to the ketogenic diet), betatrophin was significantly reduced by 15% and 27% when obese PCOS women adhered to 3 and 6 months of the ketogenic diet, respectively. Furthermore, endotrophin was significantly reduced by 19% and 34% when obese PCOS women adhered to 3 and 6 months of the ketogenic diet, respectively. Conversely, meteorin-like protein significantly surged by 10% and 19% when obese PCOS women adhered to 3 and 6 months of the ketogenic diet, respectively. Our findings suggested that the ketogenic diet and its advantageous impacts can serve as supplementary management to control PCOS complications.