Background: Gemcitabine plus cisplatin (GC) therapy is the standard of care for advanced biliary tract cancer (BTC). However, GC is considered to be toxic because of nausea, vomiting, appetite loss and inconvenient due to requiring hydration before and after cisplatin administration. Our previous JCOG0805 trial, a randomized phase II selection design study of gemcitabine plus S-1 combination therapy (GS) vs. S-1, demonstrated superiority of GS over S-1 in terms of 1-year survival with acceptable toxicity profile and showed GS to be a more promising regimen. This phase III study aims to confirm the non-inferiority of GS to GC in terms of overall survival in patients with recurrent or unresectable BTC. Methods: Eligibility criteria include chemotherapy-naïve patients with recurrent or unresectable biliary tract adenocarcinoma (gallbladder, intrahepatic biliary tract, extrahepatic biliary tract, or ampulla of Vater), an Eastern Cooperative Oncology Group performance status of 0–1, and adequate organ function. Eligible patients are randomized into either GC arm or GS arm. In the GS arm, 1000 mg/m² of gemcitabine is infused on days 1 and 8, and 30 mg/m² of S-1 is administered orally twice a day from days 1 to 14; the regimen is repeated every 3 weeks. In the GC arm, 1000 mg/m² of gemcitabine and 25 mg/m² of cisplatin are infused on days 1 and 8 and repeated every 3 weeks. The primary endpoint is overall survival and the secondary endpoints are progression-free survival, %response rate, %planned dose, adverse events, clinically relevant adverse events defined as any of grade 2 or more fatigue, appetite loss, nausea, vomiting, mucositis, diarrhea, and serious adverse events. The sample size was calculated to be 350 (175 patients per arm), with a one-sided alpha of 5%, a power of >=80%, assumed median survival time of 11.2 months in GC and of 13 months in GS, an non-inferiority margin of 1.155 in terms of hazard ratio, an accrual period of 4 years, and a follow-up period of 1 year. Twenty-eight institutions are participating in this study. The study was activated in May 2013. Clinical trial information: UMIN000010667.