The purpose of this study is to investigate the effect of clinical features including duration of FM and sexual partnership, and severity of pain, anxiety, and depression on the severity of sexual dysfunction in women with Fibromyalgia (FM). This cross-sectional study was conducted on 130 female patients with FM, who were admitted to Physical Therapy and Rehabilitation Polyclinic in August and September 2015, and 60 healthy controls. The data was collected with Beck Depression Inventory (BDI), Beck Anxiety Inventory (BAI), Women Sexual Function Index (FSFI), Fibromyalgia Impact Questionnaire (FIQ) and Visual Analogue Scale (VAS). Evaluating FM and control group according to the FSFI Score, it was found that 103 (84.4%) and 19 (15.6%) had sexual dysfunction, respectively. The median scores of FSFI scale and subscale, and VAS in the FM patients were significantly higher than those in the control group (p < 0.05). The mean scores of FIQ, BAI, and BDI in the FM patients were significantly higher than those in the control group (p < 0.05). The FSFI score was significantly predicted by FIQ, BAI, duration, and duration of partnership. FSFI score has a negative correlation with BAI score, disease duration and duration of partnership. This study supports that FM may affect all domains of sexual function. In our clinical settings, multiple regression analysis reveals that the duration and severity of FM and duration of sexual partnership, and severity of anxiety but not severity of pain and depression can increase the severity of sexual dysfunction. Knowledge about meaningful contributing factors of duration of FM and sexual partnership, and severity of FM and anxiety may be helpful for physicians for determining correct strategies for prevention and management of sexual dysfunction in FM.