Biliary tract cancer is an aggressive gastrointestinal malignancy with a dismal prognosis. Combined chemotherapy with gemcitabine and cisplatin is the gold standard of first-line treatment for patients with advanced biliary tract cancer, while second-line therapy remains inconclusive. We aimed to evaluate the effects of apatinib as a second-line regimen in patients with advanced biliary tract cancer. We retrospectively analyzed 18 patients with advanced biliary tract cancer who failed first-line therapy with gemcitabine alone or gemcitabine combined with cisplatin and received second-line treatment with apatinib from June 2016 to October 2017. Adverse events, progression-free survival, objective response rate, and disease control rate were documented and evaluated. All patients were followed up until progression of the disease.All patients were included in the efficacy analysis, including 6 drop-out cases. The 1-month tumor response assessment showed an objective response rate of 33% and a disease control rate of 72%. At a 6-month follow-up, a disease control rate of 44% was observed. The cohort achieved a median progression-free survival of 8 months; for gallbladder carcinoma of 2.5 months; for cholangiocarcinoma of 8 months. Fatigue, hypertension, and proteinuria were the most frequently occurring apatinib-related toxicities. Nine cases of grade 3 adverse effects were recorded, and no bleeding cases or treatment-related death were observed. This retrospective analysis showed favorable outcome and manageable toxicities of apatinib treatment in a second-line setting in patients with advanced biliary tract cancer. Perspective studies are needed to confirm the results from this study.