Echinococcus multilocularis has been spreading through Europe but has not yet been reported in Croatia. We report the results of a surveillance programme to detect E. multilocularis in red foxes (Vulpes vulpes) in different parts of Croatia. PCR-based screening of faecal samples from 238 red foxes in 2015 and 150 in 2016 indicate prevalences of 7.5% in 2015 and 6.6% in 2016 (overall 7.2%, CI 4.9 to 10.3). Positive samples were confirmed by sequencing parts of the nad1 gene and the gene encoding mitochondrial 12S rRNA. Geographic locations of all examined and positive cases were mapped to provide data on the distribution of E. multilocularis. Our results provide the first detection of E. multilocularis in Croatia and extend the southern boundary of this parasite's endemic area.