Intestinal metaplasia is regarded as a possible predisposing factor of cancer, particularly of the intestinal type adenocarcinoma. The clinicopathologic features of intestinal type adenocarcinoma have been well documented in the stomach, and intestinal metaplasia and intestinal type adenocarcinoma has also been reported in the gallbladder. However, regarding the intrahepatic bile ducts, the clinicopathologic features are not yet clear and there have been no reports in English literature on intestinal type intrahepatic cholangiocarcinoma. We report a case of intestinal type cholangiocarcinoma associated with hepatolithiasis in the large intrahepatic bile duct. The tumor showed mainly intraductal papillary growth primarily composed of absorptive columnar cells. Particularly, Paneth cell metaplasia of carcinoma cells was widespread, and goblet cells and neuroendocrine cells were also observed in the carcinoma tissue, to a varied degree. It showed an intraluminal spread along the dilated intrahepatic ducts with minimal ductal stromal invasion. In the vicinity of the tumor, intestinal metaplasia was also identified in the adjacent hyperplastic and dysplastic bile duct epithelium. Some bile ducts contained stones and the mural glands of the bile ducts showed hyperplastic change secondary to stones. This case is considered to provide the evidence supporting the concept of the metaplasia-dysplasia-carcinoma sequence via intestinal metaplasia in the stone-containing intrahepatic bile ducts.