Congenital choledochal cyst is occasionally complicated by carcinomatous transformation, mostly adenocarcinoma. Adenosquamous carcinoma arising in a congenital choledochal cyst is very rare. The author herein reports an adenosquamous carcinoma arising in congenital choledochal cyst associated with pancreatico-biliary maljunction. A 34-year-old man with congenital choledochal cyst and recurrent cholangitis had been followed up, and was admitted to hospital to undergo testing for cancer. Imaging modalities including computed tomography, magnetic resonance imaging and endoscopic retrograde cholangiography showed an elevated lesion in the choledochal cyst. Because clinical cytology of bile indicated malignant cells, pancreatico-duodenectomy, cholecystectomy, and resection of the choledochal cyst were performed. Grossly, the choledochal cyst was type I, and its size was 8 × 10 cm. Anomalous pancreatico-biliary ductal union was recognized. An elevated lesion was recognized in the choledochal cyst. Histologically, the lesion was composed of a squamous cell carcinoma element and an adenocarcinoma element; a gradual transition was recognized between the two. The squamous cell carcinoma element contained microcytic cells with mucins. On immunohistochemistry the adenocarcinoma element and microcytic cells were positive for CEA, but the squamous cell carcinoma element was negative for CEA. Both elements were positive for CA19-9. Ki-67 labeling was 53% in the adenocarcinoma element and 48% in the squamous cell carcinoma element. p53 protein was negative in both elements. At the time of writing, the patient was alive after 25 months without recurrence or metastasis. The present case is the second case of adenosquamous carcinoma arising in congenital choledochal cyst in the English-language literature.