Lymphoepithelioma-like cholangiocarcinoma (LELCC) is a rare subtype of carcinoma that is poorly reported. We report a case of LELCC in a 28-year-old female with chronic hepatitis B. She underwent secondary microwave ablation for residual tumor following the failure of radiofrequency ablation (RFA). Image fusion technology was used to accurately diagnose that the second lesion represented residual tumor. This case is the second successful application of microwave ablation in the treatment of LELCC. We first reviewed the ultrasonographic features of LELCC. We report this case to improve our understanding of this disease and provide evidence for its clinical treatment.