The oral fluoropyrimidine, S-1, combined with or without gemcitabine is considered to be a promising agent for treating advanced biliary tract cancer; gemcitabine plus cisplatin is the current standard regimen. This randomized phase II trial was designed to evaluate the safety and efficacy of two regimens: gemcitabine plus S-1 (GS) (gemcitabine: 1000 mg/m2, day 1 and day 8; S-1: 60 mg/m2, twice daily on days 1–14, repeated every 3 weeks); and S-1 (80 mg/m2, days 1–28, given orally twice daily for 4 weeks, followed by a 2-week rest, repeated every 6 weeks). The regimen with a higher 1-year survival would be selected for a subsequent phase III trial. Between February 2009 and April 2010, 101 patients were randomized. For the GS (n= 51) and S-1 (n= 50) arms, the 1-year survival was 52.9% (95% confidence interval, 38.5–65.5) and 40.0% (95% confidence interval, 26.5–53.1), and the median survival times were 12.5 and 9.0 months, respectively. Grade 3/4 hematological toxicities were more frequent in the GS arm (leucocytes 29.4%, neutrophils 60.8%, hemoglobin 11.8%, platelets 11.8%) than in the S-1 arm (leucocytes 2.0%, neutrophils 4.0%, hemoglobin 4.0%, platelets 4.0%). Although two treatment-related deaths occurred in the GS arm, all other grade 3/4 non-hematological toxicities were reversible. In conclusion, GS was considered to be more promising and was selected as the test regimen for a subsequent phase III trial comparing GS with gemcitabine plus cisplatin combination therapy. This study was registered at the UMIN Clinical Trials Registry as UMIN 000001685 (http://www.umin.ac.jp/ctr/index.htm).