In East Asia, a strong winter monsoon and high baroclinicity cause enhanced cyclone activity, which has been the subject of intensive study. Despite the high frequency of genesis of mesoscale cyclones in this area, most of the studies on the decadal timescale have focused only on synoptic‐scale cyclones. To clarify the interannual variation of the passage of winter cyclones including synoptic‐scale and mesoscale cyclones over and around Japan, a tracking algorithm was applied to 62 winter seasons (December–March) from 1958/1959 to 2019/2020. During the study period, the passage of cyclones around northern Japan showed a decreasing trend. Most cyclones that pass around northern Japan are generated over the northern part of the Sea of Japan, which is an area where cyclogenesis has decreased during the study period. Weather pattern classification based on synoptic scale atmospheric conditions revealed that passage of upper‐level troughs and occurrence of lower‐level cold air outbreaks are the preferential conditions for cyclogenesis in this region. In addition, the intensity of the cold air outbreak in this region was weakened during the study period. These results suggest that changes in atmospheric conditions due to climate change have reduced mesocyclone genesis over the northern Sea of Japan, resulting in the reduction in the number of cyclones passing over and around northern Japan.