Hilar cholangiocarcinoma is a rare cancer with an increasing incidence. In the palliative setting for patients with unresectable hilar cholangiocarcinoma, photodynamic therapy (PDT) is a treatment approach. However, little is known about the role of adding systemic chemotherapy to PDT. In a phase II randomized study, 21 patients were randomly assigned to receive PDT with S-1 chemotherapy or PDT alone. The 1-year survival rate for patients treated with the combination was significantly higher than for those receiving PDT alone (76.2% versus 32%, respectively). Importantly, the overall survival was also significantly improved for patients receiving PDT and S-1 (17 months versus 8 months). Progression-free survival was also prolonged with the combination, and the treatment was well tolerated. These promising results warrant further investigation of this combination in patients with unresectable hilar cholangiocarcinoma.