Primary perivascular epithelioid cell tumors (PEComas) of the pancreas are extremely rare. We herein report our experience with a patient who had a primary PEComa of the pancreas that was diagnosed by the preoperative histopathological examination of a biopsy specimen obtained by endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA). The patient was a 43-year-old woman whose chief complaint was abdominal pain. Imaging studies revealed a pancreatic tumor. Gastrointestinal stromal tumor (GIST), solid pseudopapillary tumor and neuroendocrine tumor were considered in the differential diagnosis. A histopathological examination of a specimen of the tumor obtained using EUS-FNA showed spindle-shaped tumor cells with enlarged nuclei and eosinophilic cytoplasm. The tumor cells proliferated in a sheet-like fashion and stained positive for the melanoma-associated antigen HMB-45. A PEComa was thus diagnosed. If an adequate tumor specimen can be obtained using EUS-FNA, immunostaining may facilitate the diagnosis of extremely rare diseases and therefore assist in deciding the treatment policy.