Tick-borne pathogens (TBPs) are an emerging concern to humans and animals in the Republic of Korea, especially within the military zones of Gangwon Province, a mountainous region abundant with wild fauna and ticks. This study aimed to detect six TBPs in military working dogs (MWDs) and ticks in this region using Nested polymerase chain reaction (nested PCR) and sequencing. The targeted pathogens included Anaplasma phagocytophilum, Bartonella henselae, Borrelia spp., Orientia tsutsugamushi, Severe fever with thrombocytopenia syndrome virus (SFTSV) and tick-borne encephalitis virus (TBEV). A total of 164 serum samples from MWDs were collected at the Korean Army Military working dog training center and 1418 ticks were collected at various training sites between June 2021 and August 2022. Haemaphysalis longicornis was identified as the predominant species (98.3%, n = 1394), followed by Haemaphysalis flava (1.6%, n = 22) and Ixodes nipponensis (0.1%, n = 2). This study detected A. phagocytophilum and Borrelia theileri in 1.4% (1/72) of the tick pools and detected SFTSV in 0.6% (1/164) of MWD serum samples. The MWD found to be infected with SFTS was a German Shepherd, but showed no significant clinical signs, with a normal complete blood count (CBC). In the phylogenetic analysis, three sequences were acquired. One sequence (OR865211) exhibited 100% homology with 16S rRNA of A. phagocytophilum identified from animals and human patients in the Republic of Korea. Another sequence (OR865152) displayed 99.34%–100% sequence similarity with 16S rRNA of B. theileri fragments. The third sequence (OR865115), which belongs to the SFTS B-1 genotype, showed 94.7% sequence similarity to a strain identified in the Republic of Korea (KY789441).