Background Lymphoepithelioma-like carcinoma(LELCC) is a rare variant of intrahepatic cholangiocarcinoma (ICC), LELCC is composed of prominently reactive lymphoid infiltration and scattered malignant epithelial cells, which may lead to misdiagnosis of pathologist, especially on rapid freezing during operation. Recognizing the tumor is important to avoid misdiagnosis. Case presentation We report a case of LELCC in a 53-year-old Chinese female patient with EBV infection, who was found to have a nodules in the junction of the left and right lobes of the liver on abdominal Computed tomography(CT) and magnetic resonance imaging(MRI). Microscopically, the boundary of the tumor was clear with incomplete fibrous capsule around the tumor, the tumor was arranged in a nest or tubular gland, tumor cells were cubic, with vesicular nuclei, prominent nucleoli, rare mitotic figures, and abundant lymphoid infiltration and lymphofollicular formation. Immunohistochemically, tumor cells were diffusely positive for biliary-type cytokeratins (CK7, CK19), CK8,CK18,Ki-67 proliferation index (about 20%) and negative for CK20, polyclonal carcinoembryonic antigen(CEA) and CD34, hepatic marker (HepPar-1), The tumor-infifiltrating lymphocytes are predominant for CD3 and CD45RO-positive T cells, CD20 and CD79α are positive scattered in the germinal center and surrounding areas. In situ hybridization, EBV-encoded RNA (EBER) was strongly positive in tumor cells. Conclusions The diagnosis of LELCC should be combined with histopathology, immunohistochemistry and EBER detection. There are limited literature reports on the pathological diagnosis and differential diagnosis, additional studies will be needed to needed to clarify the clinicopathologic features, immunophenotype, and differential diagnosis of this disease. It is necessary to master the diagnostic criteria to avoid misdiagnosis for pathologist.