Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children. It is located mainly in the head and neck, extremities and trunk, rarely achieving the biliary tract (1%). The clinical presentation is characterized by obstructive jaundice, abdominal pain and palpable mass. The prognosis is favourable when being early diagnosed. The main differential diagnosis is the choledochal cyst. We bring a case report about a patient with biliary tract rhabdomyosarcoma, diagnosed and treated for 1 year as choledochal cyst, presenting obstructive jaundice for one year. A hepatic biopsy was done, showing hepatic fibrosis. He presented clinical worsening and was referred for liver transplant. An exploratory laparotomy was done before planning the transplant, which showed a biliary tract mass, followed by a biopsy. The anatomopathological result was RMS. Biliary tract RMS is a rare entity that should be included in the differential diagnosis of obstructive jaundice in children. Because of its similarity with choledochal cyst, pediatricians and surgeons should consider this hypothesis, for adequate investigation and treatment.