Background Polycystic ovary syndrome (PCOS) is the most common endocrinological disease affecting women in the reproductive age. Non-alcoholic fatty pancreas disease (NAFPD) can promote many aspects of pancreatic dysfunction. The present study aimed to determine the prevalence of NAFPD and to identify its association with clinical and biochemical parameters in PCOS patients. Methods The present study included 150 patients with PCOS and 150 age-matched healthy controls. All patients were submitted to careful history taking and thorough clinical examination. Performed laboratory investigations included fasting and postprandial blood glucose, lipid profile, liver function tests, serum prolactin and total testosterone. Fatty pancreas was diagnosed using abdominal ultrasound. Results Among PCOS women, NAFPD was diagnosed in 57 women (38.0%) in contrast to 18 women (12.0%) in the control group (p < 0.001). Patients with NAFPD were significantly older [median (IQR): 38.0 (35.0–43.0) versus 29.0 (25.5–33.0) years, p = 0.001] with higher BMI [median (IQR): 31.5 (29.1–34.7) versus 30.4 (28.6–32.4) kg/m 2 , 0.042]. Moreover, they had significantly higher frequency of metabolic syndrome (84.2% versus 54.8%, p = 0.001), insulin resistance (68.4% versus 26.9%, p < 0.001) and severe NAFLD (22.8% versus 2.2%, p < 0.001). NAFPD patients had significantly lower sex hormone binding globulin (SHBG) [median (IQR): 36.0 (30.8–40.7) versus 38.1 (35.15–42.7), p = 0.002] and significantly higher free androgen index (FAI) [median (IQR): 4.08 (3.3–4.92) versus 3.47 (3.12–4.05), p < 0.001]. Conclusion NAFPD is prevalent PCOS. It is related to metabolic syndrome, insulin resistance, dyslipidemia and hyperandrogenism.