Current studies have focused on the association of fibromyalgia syndrome (FMS) and obsctructive sleep apnea syndrome (OSAS). Results of these studies on the effect of this association have been inconsistent. The current study aimed to investigate the effect of FMS on OSAS regarding sleep quality, pressure pain threshold, fatigue, daytime symptoms, anxiety, and depression, and also to determine the relationship between OSAS severity and FMS. In a cross-sectional design, patients diagnosed with OSAS were evaluated in two groups comparing those with and those without FMS. Data on demographics, headache, morning fatigue, and chronic pain duration were collected. Questionnaires including the Fatigue Severity Scale (FSS), Fibromyalgia Impact Questionnaire (FIQ), Beck Depression Inventory (BDI), and Beck Anxiety Inventory (BAI) were completed. Pressure pain threshold, tender points, and polysomnographic data were recorded. Of 69 patients, 27 were diagnosed with FMS + OSAS and 42 were diagnosed as OSAS only. Statistically significant differences were found between the two groups in VAS, pain duration, morning fatigue, headache, BAI, tender point count, FIQ and FSS scores, and algometer measurements. All polysomnografic data were compared, and no statistically significant differences were found between the two groups. There were no statistically significant differences in the algometer, BDI, BAI, FIQ, and FSS scores when analyzed according to the severity of OSAS. The findings suggest that FMS has no effect on polysomnographic parameters of OSAS. Headache, daytime fatigue, anxiety, depression, pain duration, and pain intensity are higher while the pressure pain threshold is lower when FMS is present. No correlation was found between OSAS severity and FMS, fatigue, pressure pain threshold, depression, and anxiety. NCT05367167/date: April 8, 2022.