We aimed to identify the clinicopathological features of lymphoepithelioma-like intrahepatic cholangiocarcinoma (LEL-ICC), and EBV latency pattern and sequence variations of EBV-associated LEL-ICC. The clinical and pathological information of nine cases of LEL-ICC diagnosed in Department of Pathology, the Third Affiliated Hospital of Sun Yat-sen University from January 2015 to October 2022 were collected. EBV latency pattern and sequence variations of EBV-associated LEL-ICC were investigated. There were 3 males and 6 females with a median age of 47 years in our cases. The morphological feature was the poorly differentiated or undifferentiated tumor cells surrounded by densely tumor infiltrating lymphocytes. Immunohistochemical staining showed the tumor cells were positive for CK7 and/or CK19, negative for HepPar-1 and Arginase-1. Eight cases showed positive nuclear signal in tumor cells by in situ hybridization of EBER. Five surgical specimens of EBV-associated LEL-ICC were positive for EBNA1 and negative for EBNA2, LMP1 and ZEBRA by immunohistochemestry. The type A strain, type f, type I, and del-LMP1 variants were found in EBV-associated LEL-ICC patients. LEL-ICC is a rare subtype of ICC and the accurate diagnosis mainly depends on typical histopathology, immunohistochemistry and in situ hybridization for EBER. The latency pattern in EBV-associated LEL-ICC patients was probably latency type I, the mainly EBV genotypes were perhaps type A strain, type f, type I and del-LMP1 variants.