In this study, we investigated tick-borne pathogens in blood samples collected from 34 wild animals from six different regions in the Republic of Korea, including 18 Korean water deer (Hydropotes inermis argyropus), 15 Korean raccoon dogs (Nyctereutes procyonoides koreensis), and one roe deer (Capreolus capreolus). Polymerase chain reaction revealed Anaplasma spp. infection in 11 Korean water deer, one roe deer, and one Korean raccoon dog. Theileria spp. infection was detected in 14 Korean water deer and one roe deer. Co-infection with two pathogens (Anaplasma spp. and Theileria spp.) was identified in 10 Korean water deer and one roe deer. Ehrlichia and Rickettsia spp. infections were not detected in any of the animals. Genetic analysis showed that Anaplasma sp., A. bovis, A. phagocytophilum, Theileria sp., T. cervi, and T. luwenshuni were present in these animals. Our results showed that T. luwenshuni was the most prevalent species found in Korean water deer. Interestingly, our findings demonstrated that the Korean raccoon dog was a reservoir for anaplasmosis, indicating that transmission of A. bovis was not restricted to host species. The roe deer was found to be infected with a type F T. cervi strain. To the best of our knowledge, this study is the first to report A. bovis infection in Korean raccoon dogs, T. cervi in roe deer, and T. luwenshuni in Korean water deer. Our results indicated that wild animals represent possible reservoirs for these tick-borne pathogens, thus playing an important role in the transmission of tick-borne diseases (TBDs) in domestic animals, livestock, and humans. Furthermore, our findings highlight the risk associated with introducing new pathogens as well as the role of wild animals in the transmission and spread of these zoonotic TBD pathogens.