We report on a 16-year old girl with postoperative biliary atresia developing cystic dilatation of the intrahepatic biliary system (CDIB) with abdominal pain, which was relieved after percutaneous transhepatic biliary drainage (PTBD). A cyst was detected in segment 4 of the liver at the age of 14 years. She developed severe right hypochondralgia, subfever and liver dysfunction. Percutaneous cholangiogram showed a solitary cyst without communication and a PTBD tube was placed within the cyst. After lavage of the cyst through PTBD, CDIB was re-communicated with the intestine and the pain was relieved with reduction of the cyst size. From this experience, PTBD may be a less invasive treatment as the first choice for non-communicating CDIB and may alleviate the symptoms when recommunication with the intestine is obtained.