The incidence and several risk factors of biliary complication (BC) following pediatric liver transplantation (LT) are widely known, but data on long-term outcomes and management is limited. This retrospective study aimed to investigate the incidence, associated risk factors, management, and outcomes of early and late BC in pediatric LT. This study enrolled 134 pediatric patients (< 18 years old) who underwent LT at a tertiary care center in Taiwan between January 2001 and December 2015. Diagnosis of BC was based on clinical, biochemical, and radiologic examinations. Clinical data and chart records were reviewed and compared between the groups. Among the 134 children, 21 children (15.7%) had BC after LT. Nine children had early complications, including leakage plus stricture (n = 2), stricture only (n = 2), and leakage only (n = 5). Twelve children had late BC; all of whom had anastomotic stricture. Of the 21 patients with BC, 11 patients (52.4%) were treated without surgery. The median time of first treatment for BC was 6.5 months (range, 11 days to 6.2 years). Five of the 9 patients with early complications and two of the 12 patients with late complications died of biliary tract infection. The major risk factors of BC in pediatric LT were (1) recipient age > 2 years, (2) Kasai portoenterostomy revision, and (3) hepatic artery thrombosis. Several risk factors of BC in pediatric LT were identified. Children with early BC appeared to have relatively unfavorable outcomes. However, late BC treated by either radiological or surgical methods appeared to have a relatively good long-term prognosis.