Canine circovirus (CanineCV) is a recently discovered pathogen increasingly detected in domestic dogs and wild carnivores and is associated with various clinical manifestations. Wild carnivores such as golden jackals (Canis aureus) and red foxes (Vulpes vulpes) are widespread opportunistic species and known reservoirs of numerous pathogens. In a previous study, we molecularly characterized nine CanineCV strains from golden jackals and one from a red fox collected in Serbia. Although the initial phylogenetic analysis indicated the presence of two viral genotypes (genotypes 4 and 5), a new time-scaled phylogenetic reconstruction has revealed a more complex evolutionary landscape. Using BEAST, we identified three genetically divergent, well-supported monophyletic groups among the CanineCV strains from wild carnivores and documented at least four independent introduction events of the virus into the studied wildlife population. Within genotype 5, the jackal strains form a lineage whose most recent common ancestor (MRCA) dates to approximately 2003 and is evolutionarily linked to an older lineage (≈ 1975) of northern-European origin observed in foxes. Genotype 4 in jackals comprises two evolutionarily distinct lineages: an older lineage with an MRCA around 1987 that clusters with canine and wild-carnivore sequences from Europe and the Americas (dominated by Italian strains) and a more recent lineage (≈ 2017) consistent with a recent viral introduction. These findings underscore the genetic diversity and complex circulation pathways of CanineCV in southeastern Europe and highlight the value of time-calibrated phylogenetic methods for investigating viruses in wildlife hosts.