Bornaviruses are neurotropic, negative-sense RNA viruses with zoonotic potential, notably Borna disease virus 1 (BoDV-1) and variegated squirrel bornavirus 1 (VSBV-1). BoDV-1 is endemic in certain regions of Central Europe and maintained in bicolored white-toothed shrews, but its presence in Croatia has not been investigated. Given Croatia’s diverse biogeography and the prevalence of rodent-borne diseases, this study aimed to investigate the presence of orthobornaviruses in wild canids and mustelids. Brain samples from red foxes (Vulpes vulpes), golden jackals (Canis aureus moreoticus), wolves (Canis lupus), martens (Martes martes) and badgers (Meles meles) were analysed using pan-bornavirus RT-PCR. Despite successful RNA extraction and internal control amplification, bornavirus RNA was not detected in any of the 860 animal samples tested. Although no orthobornavirus RNA was detected, the results still provide valuable information: bornavirus infections appear to be absent or extremely rare in Croatian wild canids and mustelids. By excluding these species as current potential reservoir hosts, this study helps to refine the geographical extent of bornavirus endemicity and emphasises the importance of continuous One Health surveillance in regions with favourable ecological conditions for zoonotic spillover.