Hepatozoon canis is a protozoan tick-borne parasite infecting domestic and wild canids, including foxes, wolves, and jackals. It is mainly found in dogs but has also been detected in several wild carnivores, including foxes, wolves, and jackals. Host transmission primarily occurs through the ingestion of infected ticks, typically Rhipicephalus sanguineus, with documented instances of transplacental transmission from infected females to cubs. In Serbia, the golden jackal is common throughout the country, and its population has increased in recent years. Previous research has documented the presence of several vector-borne pathogens in the jackal population in Serbia, so we conducted this study to determine the presence, prevalence, and genetic variability of H. canis. Over eleven years (2010–2020), 114 animal samples were collected from 23 localities in Serbia. A total of 90/114 (78.95%) jackals were positive for H. canis, and they came from 22 localities. Among 15 juveniles, almost half (6/15 (40%)) tested positive for H. canis. In addition to the high prevalence, high genetic variability of the pathogen was also found. According to the mutated positions, four sequence types (S4–S7) of H. canis were determined. Based on our earlier research on the grey wolf and on this study, it can be observed that various sequence types of H. canis circulate within wild canid populations in Serbia. The prevalence of H. canis infection in wild carnivores raises significant concerns for wildlife conservation and animal health. Infected animals may act as reservoirs for the disease, posing a potential risk to domestic animals by acting as a source of infection.