We evaluated the effects of forest thinning on peak flow and recession characteristics of storm runoff in headwater catchments at Mie Prefecture, Japan. In catchment M5, 58.3% of stems were removed, whereas catchment M4 remained untreated as a control catchment. Storm precipitation and runoff was monitored from June 2004 to January 2007 for the pre-thinning period (113 events) and from March 2007 to June 2009 for post-thinning (103 events). Based on paired-catchment analysis between M5 and M4, volumes of peak flow did not increase significantly after thinning. Recession constant K increased, while recession time of storm runoff did not differ between pre- and post-thinning periods. Storm hydrograph recession tended to be more gradual (i.e., higher K values) after thinning due to increases in available soil water associated with higher net precipitation and decreased evapotranspiration. The lack of changes in peak flow can be attributed to the minimal soil disturbance during thinning. Our hydrograph analysis in paired catchments indicates that thinning may alter specific internal hydrological pathways, such as subsurface flow and groundwater flow.