Few studies have compared percutaneous biliary stenting (PBS) and endoscopic biliary stenting (EBS) in terms of long-term effects on cholangiocarcinoma (CC), and few have systematically evaluated outcome associations in Taiwan. This study aimed to compare long-term outcomes between two treatments for unresectable CC: PBS and EBS. After propensity score matching (PSM) to reduce the effect of selection bias, 1002 CC patients were included in this analysis: 501 in the PBS group and 501 in the EBS group. The Kaplan-Meier method was used to construct the survival curve for all CC patients, and the Cox proportional hazards model was used for multivariate assessment of outcome predictors. After PSM, group comparisons revealed a significantly longer length of stay in the PBS group compared to the EBS group (25 days vs. 19 days, respectively; p < 0.001). Hospital costs were also significantly higher in the PBS group than in the EBS group (US$126,575 vs. US$89,326, respectively; p < 0.001). The median survival time was 3.7 months in all CC patients, 3.5 months in the PBS group, and 4.0 months in the EBS group. The 1-year, 3-year, and 5-year survival rates were 17.6%, 6.1%, and 3.2% in all CC patients; 16.6%, 4.8%, and 3.2% in the PBS group; and 18.6%, 7.27%, and 3% in the EBS group, respectively. The most important predictor of survival is extrahepatic CC. Medical professionals and healthcare providers should carefully consider the use of EBS for initial treatment of obstructive jaundice in patients with unresectable CC.