Background The mutations associated with metastasis in advanced-stage cholangiocarcinoma (CCA) have not been investigated. Objective To explore mutations in patients with advanced CCA and independent factors related to metastasis. Methods This retrospective study performed next-generation sequencing of tumor specimens from patients with advanced CCA treated between January 2017 and December 2019. Tumor mutational burden (TMB), microsatellite instability, and programmed cell death ligand (PD-L)1 positivity were determined. Factors independently associated with metastasis were explored via logistic regression. Results Ninety-one patients were included in this study. TP53 mutation frequencies were significantly higher in extrahepatic than intrahepatic CCA, while ARID1A mutations were significantly more frequent in intrahepatic CCA. Mutation frequencies in six selected genes did not differ according to patient age or sex. SMAD4 mutations were significantly less frequent in stage IV cancer; ARID1A and PBRM1 mutation frequencies were significantly higher in TMB >10 tumors. PBRM1 mutation frequencies were significantly higher in PD-L1-positive tumors, but lower in patients with metastasis. Multivariable analysis showed that a history of biliary surgery, SMAD4 mutations, and PBRM1 mutations were independently associated with CCA metastasis. Conclusions A history of biliary surgery and mutations in SMAD4 and PBRM1 are independent protective factors for metastasis in patients with advanced CCA.