To elucidate the epidemiology of murine typhus, which is infrequently reported in Japan, we conducted a cross-sectional study involving 2,382 residents of rickettsiosis-endemic areas in Honshu Island during August–November 2020.Rickettsia typhiseroprevalence rate was higher than that ofOrientia tsutsugamushi, indicating that murine typhus is a neglected disease.