Hepatectomy with vascular reconstruction for biliary malignancy remains controversial. This study aimed to clarify the indications for surgery. Patients with advanced hilar bile duct cancer (HBDC) (n = 26) and gallbladder cancer (GBC) involving the hepatoduodenal ligament (n = 13) who underwent hepatectomy were enrolled. They were divided into two groups on the basis of whether vascular reconstruction was performed (HBDC, 10 yes vs. 16 no; GBC, 5 yes vs. 8 no). Portal vein (PV) reconstruction was performed on the right branch in seven patients and on the left branch in two; hepatic artery (HA) reconstruction was done on the right branch in 11 patients and on the left branch in 1. Five patients with HBDC and one with GBC underwent both PV and HA reconstruction. Patency rates were 88.0% and 83.3% for PV and HA reconstructions, respectively. Vascular reconstruction-related morbidity occurred in one patient with fatal liver failure owing to a portal thrombus and in two patients with multiple liver abscesses caused by arterial obstruction. Microsurgery eliminated reconstruction-related morbidity. Mortality in vascular reconstruction cases was 13.3% (2/15), and in those without reconstruction it was 8.3% (2/24). Curability rates (R0 and R1+R2) were 50.0% and 56.0% for HBDC and 40.0% and 62.5% for GBC, respectively. The 3-year survivals of HBDC patients were, respectively, 33% and 42%, and the 5-year survivals were 18% and 25%, whereas for GBC the 1-year survivals were 20% and 60% and the 2-year survivals 0% and 25%. Two patients with vascular involvement who underwent PV with HA reconstruction survived more than 3 years. Hepatectomy with vascular reconstruction for selected HBDC patients offers low surgical risk and increased survival by curable resection, but it is not recommended for advanced GBC.