Pancreatic lymphoepithelial cysts are rare, benign, non-neoplastic unilocular or multilocular cystic lesions. These circumscribed pancreatic lesions are filled with keratinous material grossly and exhibit distinct microscopic features. Pancreatic lymphoepithelial cysts are like the more common lymphoepithelial cysts of the parotid glands, which have been associated with the diffuse infiltrative lymphocytosis syndrome often seen in patients with HIV infection. However, pancreatic lymphoepithelial cysts are rare and their association with HIV infection has not been established. The presence of secondary changes in non-neoplastic cysts such as goblet cell metaplasia that was present in our case is an important feature to be included in the differential diagnosis and not to be interpreted as a mucinous neoplasm, particularly on fine-needle aspiration specimen microscopic evaluation that would impact further management. Here we describe the diagnosis and treatment of lymphoepithelial cysts in a patient who was on highly active antiretroviral therapy for HIV infection and we provide a brief literature review. Defining the clinical characteristics of lymphoepithelial cysts in patients with HIV and determining accurate preoperative diagnostic procedures will be critical for establishing effective surgical and medical approaches to treating these cysts, which differ substantially from other more serious pancreatic cystic lesions.