Because volcanic rocks have high permeability, rainfall quickly infiltrates into the ground. Perennial rivers often do not exist in volcanic areas. However, available studies elucidating hydrologic characteristics and the mechanisms of stream formation in young volcanic areas are limited in number, extent, and coverage prohibiting a comprehensive understanding of runoff formation. By measuring river discharge for two years, we examined the characteristics of surface runoff in four adjacent headwater catchments within a young volcanic area of Mt.Fuji. The runoff coefficient R is small, rainfall thresholds for discharge are large, and the lag time Tlag and duration D of rainfall-runoff events are short. These characteristics can be explained by the groundwater flow as the dominant runoff mechanism with high hydraulic conductivity. Due to differences in topography and the depth of groundwater, some differences existed amongst the four adjacent catchments. In addition, a comparison of runoff characteristics between the young volcanic headwater catchments (VHCs) and non-volcanic headwater catchments (NVHCs) reported in other studies established that young VHCs have a smaller R, a shorter Tlag and D, and a larger runoff threshold for storm runoff than NVHCs. These differences are attributed to differences in the hydraulic conductivity of the underlying geology. These findings should help improve hydrological models and river structures for flood prevention.