Scrub typhus (ST) and Japanese spotted fever (JSF) are endemic rickettsioses in Japan, whereas murine typhus (MT) has been slightly reported over the last 50 years. To elucidate the epidemiology and risk factors of MT, we conducted a cross-sectional study of residents in the southern Boso Peninsula, a rickettsia-endemic region, from August to November 2020, using their sera, questionnaires, residential addresses, and geographic information. A total of 2,382 residents were included in the study. The seroprevalence of MT was higher than that of ST (11.3% vs. 7.9%), with a prevalence ratio of 1.42 (p<0.001). In addition, exposure to bushes and living in sparsely populated areas are significant risk factors for MT. These findings indicate that MT is a neglected disease; hence, patients with suspected rickettsial infections, especially those with risk factors, should undergo comprehensive rickettsial infection testing, including MT testing.