Objective: The purpose of this study was to determine the efficacy and safety of infusional 5-fluorouracil (5-FU), doxorubicin, and mitomycin-C (iFAM) as salvage chemotherapy in biliary tract cancer (BTC) and to identify prognostic factors. Methods: Fifty patients received 5-FU 800 mg/m2 over 10 h on days 1–5, doxorubicin 30 mg/m2 on day 1 and mitomycin-C 8 mg/m2 on day 1, every 4 weeks. The primary endpoint was the overall survival (OS) rate at 6 months. Results: The responses to iFAM were as follows: partial response in 2 patients (4.2%) and stable disease in 9 patients (18.7%). The median progression-free survival and OS were 2.2 months and 5.6 months, respectively. The 6-month OS rate was 48%. Grade 3/4 adverse events included neutropenia (10%), thrombocytopenia (8%), and anemia (2%). Based on multivariate analysis, Eastern Cooperative Oncology Group (ECOG) performance status, serum albumin, and response to previous chemotherapy were significantly associated with OS. Three risk groups based on the number of 3 poor prognostic factors (0 vs. 1 vs. 2–3) were well correlated to OS (8.7 vs. 5.5 vs. 2.4 months, respectively; p = 0.0002). Conclusions: iFAM as salvage regimen has modest effect and tolerable toxicity in advanced BTC. The described risk group classification may help guide treatment plans.