One way in which invasive alien species affect their environment is by acting as pathogen hosts. Pathogens limited by the availability of the native host species can profit from the presence of additional hosts. The muskrat (Ondatra zibethicus) is known to act as an intermediate host for the fox tapeworm (Echinococcus multilocularis). From 2009 to 2017, 15,402 muskrats caught in Flanders and across the border with Wallonia and France were collected and dissected with the aim of understanding the prevalence of this parasite in muskrats. Visual examination of the livers revealed 202 infected animals (1.31%). Out of the 9421 animals caught in Flanders, we found 82 individuals (0.87%) infected with E. multilocularis. No increase in prevalence was observed during this study. All of the infected animals in Flanders were found in municipalities along the Walloon border. We did not observe a northward spread of E. multilocularis infection from Wallonia to Flanders. We hypothesise that the low prevalence is the result of the reduced availability of intermediate hosts and the successful control programme which is keeping muskrat densities in the centre of the region at low levels and is preventing influx from other areas. Our results illustrate that muskrats are good sentinels for E. multilocularis and regular screening can gain valuable insight into the spread of this zoonosis.