ABSTRACTThe spatial and temporal variations of cumulonimbus clouds (Cbs) that produce lightning have mesoscale characteristics due to the nature of Cbs and the influence of topography; however, previous studies have lacked a mesoscale perspective because historical lightning observations relied on human observation. In this study, mesoscale variations in the number of thunder days (TDs) over the Japanese Archipelago over a 56‐year period were investigated using manned observation data (Period 1: 1954–1963) and radio‐wave observation data (Period 2: 2010–2019). A comparison of the two periods of Period 1 and Period 2 revealed that the locations of mesoscale areas with high TDs did not change significantly; however, the number of TDs increased in most mesoscale areas and it was not possible to identify any mesoscale areas with a significant decreasing trend. The characteristics of mesoscale variation varied with the season as follows: (1) Winter (November–January): the number of TDs along the coastal lands of the Sea of Japan increased significantly. The variations in the synoptic‐scale winter pressure pattern with low stability were one of the factors contributing to the increasing trend of TDs. (2) In the first half of the Baiu season (June), the number of TDs increased in two regions: one region was the south of Japan associated with the Baiu front, while the second region was the northern area of Japan, where the influence of the Baiu front is limited. (3) Summer (August): the number of TDs in mountainous areas tended to increase significantly, and the variation in the water vapour content was significantly correlated with the variation in the number of TDs. The number of TDs in the foothills did not increase significantly. (4) Akisame season (September): the number of TDs along the Pacific Ocean coast significantly increased.