Wild carnivores serve as reservoirs of several zoonotic Bartonella species such as Bartonella henselae, Bartonella vinsonii subsp. berkhoffii, and Bartonella rochalimae. The raccoon dog (Nyctereutes procyonoides viverrinus) is the most common native carnivore in Japan, but epidemiologic studies of Bartonella infections have not been performed in this animal species yet. Here, we report a molecular survey of B. rochalimae prevalence in 619 wild raccoon dogs captured from 2009 to 2017 in western Japan. Bartonella rochalimae DNA was detected in 7.1% (44/619) of the raccoon dogs examined by PCR targeting the rpoB and ssrA genes. All of the sequences obtained were identical in each of the genes. The prevalence of B. rochalimae by sex of the animals was 6.1% (21/344) in male and 8.4% (23/275) in female. The prevalence by year varied from 2% (1/45) in 2011 to 14% (4/28) in 2016. The prevalence (7.9%) of B. rochalimae in the raccoon dogs with sarcoptic mange tended to be higher than the prevalence (4.0%) in the animals without the infestation of mites, although the differences were not significant. Sequence analysis indicated that Japanese raccoon dogs in the area examined were infected with B. rochalimae carrying identical sequences in the rpoB and ssrA genes. In addition, the raccoon dog strain had few sequence variations in both genes compared to other known B. rochalimae strains detected in other parts of the world.