Clarifying the relationship between rainfall and runoff characteristics in mountainous areas is crucial to improving flood and sediment disaster prediction. This study investigates that relationship, focusing on meso‐scale catchments of 1–10 km2 in high‐relief mountainous regions where conventional observational data are limited. Such research requires observations in multiple adjoining watersheds due to the variability of runoff patterns in mountainous river systems. However, observations are challenging in meso‐scale catchments due to equipment loss in rivers. This study included seven observation sites with catchment areas of 0.16–9.01 km2 and relative elevations exceeding 1000 m within the Higashigochi River basin, a sub‐branch of the Oi River basin in Shizuoka Prefecture, Japan. Water level gauges were strategically installed at each of these locations to prevent loss. Peak lag time (the time difference between the rainfall and water level peaks), which is crucial to flood hydrograph definition and disaster preparedness, was assessed. The results indicate a general trend of increasing peak lag time with larger catchment area, although spatial heterogeneity was observed at small sites. This finding aligns with prior studies in meso‐scale catchments within mountainous regions with relative elevations of 450 m or less, suggesting that in such meso‐scale catchments, larger catchment area tends to result in longer peak lag times, regardless of topographic undulation. Overall, the impact of topographic undulations on peak lag time appears surprisingly modest, indicating that catchment area plays a more significant role in determining peak lag time. The observed heterogeneity of peak lag time could be attributable to the influence of bedrock groundwater discharge.