Inter‐catchment groundwater flow (IGF) plays an essential role in streamflow generation and water quality in forested headwaters. Multiple factors are thought to contribute to IGF, including climate, topographical, and geological factors. However, studies have not clarified the relationships between IGF and catchment properties in the headwater catchments due to the lack of observational data at scales smaller than 100 ha. This study examined possible factors influencing IGF using random forest analysis based on annual water balance data from 152 forested catchments ranging from 0.09 to 9400 ha in Japan. The results showed that catchment scale had the greatest influence on IGF, and IGF tended to decrease with increasing catchment area at scales of less than 10 ha. The average IGF stabilized around zero in catchments greater than 10 ha. The averaged IGF trend with catchment scale indicated more outward groundwater flow in catchments smaller than 10 ha, but no relationship between IGF and catchment size in catchments larger than 10 ha. The variability in IGF decreased with catchment size and was lowest at 10–100 ha. The decrease in variability in catchments less than 100 ha was mainly due to river confluence and the increased variability in catchments larger than 100 ha indicated potential observation errors increase in catchments of this size.