The tick-borne bacterium "Candidatus Neoehrlichia mikurensis" has recently been recognized as a human pathogen. Together with Borrelia afzelii, it is one of the most common pathogens found in the tick Ixodes ricinus. Here, we compared the epidemiologies of "Ca. Neoehrlichia mikurensis" and B. afzelii by longitudinal sampling from May to September in one of their most abundant vertebrate hosts, the bank vole (Myodes glareolus), using real-time PCR for detection and quantification. The prevalences of "Ca. Neoehrlichia mikurensis" and B. afzelii were determined to be 19% (50/261) and 22% (56/261), respectively. The prevalence of "Ca. Neoehrlichia mikurensis" increased significantly during the sampling season. The clearance rate of "Ca. Neoehrlichia mikurensis" was significantly higher than that of B. afzelii. We found a high frequency of double infections; 46% of all samples infected with "Ca. Neoehrlichia mikurensis" also had a coinfection with B. afzelii. The frequency of coinfections was significantly higher than expected from the prevalence of each pathogen. The high level of coinfections can be caused by interactions between the pathogens or might reflect variation in general susceptibility among voles.