Echinococcus multilocularis causes human alveolar echinococcus. In Japan, high prevalence of E. multilocularis among the fox population has been reported throughout Hokkaido. Accordingly, control measures, such as fox hunting and the distribution of bait containing Praziquantel, have been conducted. This study developed a transmission model for individuals in the fox population and included a stochastic infection process to assess the prevalence of E. multilocularis. To make our model realistic, we used the worm burden for each individual in the fox population. We assumed that the worm burden depends on the number of protoscoleces in a predated vole and the number of infection experiences. We carried out stochastic simulations with 1000 trials for the situations of Koshimizu and Sapporo, Hokkaido, Japan. The distribution of the worm burden among foxes obtained using the model agreed with dissection data. The simulation indicates that a careful choice of season is necessary for an effective distribution of Praziquantel-containing bait.A stochastic model for E. multilocularis, which can assess the range of the prevalence in the fox population, would be helpful in analyzing their complex life-cycle and also in designing control strategies.