Background Intrahepatic cholangiocarcinoma had been considered a contraindication for liver transplantation because of poorer outcomes. However, incidental intrahepatic cholangiocarcinoma in the explanted liver has been reported because of the difficulty of obtaining an accurate diagnosis in cirrhotic livers on preoperative imaging. Methods We conducted a nationwide survey to analyze the incidence of incidental intrahepatic cholangiocarcinoma and outcomes after liver transplantation, in Japan. Results Forty‐five of 64 institutions (70%) responded to our initial investigation. Between January 2001 and December 2015, 6627 liver transplantations were performed in these 45 institutions, with 19 cases (0.3%) of incidental intrahepatic cholangiocarcinoma reported from 12 transplant centers. Six cases were diagnosed as hepatocellular carcinoma preoperatively. The 1‐, 3‐, and 5‐year recurrence‐free survival rates were 79%, 45%, and 45%, respectively. Tumor recurrence after liver transplantation was found in 10 patients (53%). The 1‐, 3‐, and 5‐year overall survival rates were 79%, 63%, and 46%, respectively. Conclusions Intrahepatic cholangiocarcinoma at liver transplantation is associated with a high risk of recurrence and poor prognosis, even these tumors are detected incidentally in the explanted liver. Highlight Incidental intrahepatic cholangiocarcinoma in the explanted liver has been reported because of the difficulty of accurate diagnosis in cirrhotic livers on preoperative imaging. Hara and colleagues report the results of a nationwide Japanese survey. The incidence was 0.3% and the 1‐, 3‐ and 5‐year recurrence‐free survival rates were 79%, 45% and 45%, respectively.