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Abstract Background A lymphoepithelial cyst of the pancreas is a rare benign lesion that is difficult to diagnose preoperatively and challenging in distinguishing from potentially malignant cystic pancreatic neoplasms. A diagnostic step-up approach is recommended to clarify the lesion’s dignity and specify a treatment plan. Case presentation Here, we describe a case of a 51-year-old male European with a lymphoepithelial cyst of the pancreas mimicking malignant features in a mid-age male patient with abdominal pain and unintended weight loss. Conclusion Patients with indeterminate cystic pancreatic lesions should be examined by a multidisciplinary diagnostic team in a step-up approach to clarify the lesion’s entity. In the case of incidentally found lymphoepithelial cysts of the pancreas, a watchful waiting strategy might be clinically reasonable if the diagnosis is proven.