Objective: To compare the clinicopathological features and prognosis of pancreatic cystic neoplasms (PCN) between male and female patients. Methods: A total of 325 patients with histological confirmed PCN from January 2010 to October 2015 were enrolled. The clinicopathological features, laboratory examination, imaging features, treatment and prognosis were analyzed. Results: Of the 325 patients diagnosed as PCN, 104 were male and 221 were female. The average age of male patients was significantly higher than that of female patients (55.0±12.7 vs 47.9±13.4 years, P <0.001), however, the average tumor size of male patients was smaller than that of female patients (3.9±2.7 vs 4.9±3.0 cm, P =0.004). The location of PCN in male patients was predominantly located at pancreatic head and neck, and majority of male patients were mucinous cystic neoplasms. 1-year, 3-year and 5-year survival rates of patients with PCN were 98.5%, 92.6%, and 87.5%, respectively. 1-year, 3-year and 5-year survival rates of male patients were 97.8%, 84.9%, and 77.8%, however, those of female patients were 98.8%, 96.5%, and 92.2%, respectively. Female patients had better prognosis than male patients (χ 2 =5.543, P =0.019). Elevated CA19-9 (χ 2 =3.843, P =0.050), perineuronal invasion (χ 2 =6.250, P =0.012) and lymph node metastasis (χ 2 =4.529, P =0.033) were important prognostic factors for malignant mucinous cystic neoplasm. Conclusions: Male patients had low incidence of PCN, and were more common for mucinous cystic neoplasm. The long-term outcome of malignant PCN was poor. Even with complete resection, male patients still had worse prognosis. Close follow-up is recommended especially for male patients.