Background: Polycystic Ovarian Syndrome (PCOS) is a common hormonal disorder that affects approximately 5-20% of women of childbearing age. Physical and psychological changes caused by PCOS might impair women’s sexual function. Infertility is one of the most important complications that may be seen in women with PCOS. This study aimed to compare sexual function in fertile and infertile women with PCOS diagnosis.Method: This cross-sectional study was conducted on 364 fertile and 239 infertile women that diagnosed with PCOS according to the Rotterdam criteria from May 2018 to February 2019. All participants were asked to fill out included demographic survey and Female Sexual Function Index (FSFI) questionnaires.Result: The mean total FSFI score in fertile and infertile women was 23.70±6.26 and 24.65±4.04, respectively. With regard to FSFI, the differences between the two groups were not statistically significant in terms of total FSFI score, desire, lubrication, satisfaction, and arousal score (P>0.05). However, the pain score, was significantly higher in the fertile group. (3.51±1.27, 3.10±1.11, P<0.001). Conclusion: Impaired sexual function in infertile women diagnosed with PCOS can be more associated with PCOS-related complications and other concurrent factors that affects sexual function rather than infertility. It seems that the effects of infertility on sexual function can be different in infertile women according to each person's condition. Hence, screening for sexual dysfunction in women with PCOS and infertility should be deemed as a part of clinical assessment, leading to early diagnosing and improving their quality of life.