The Iriomote cat (Prionailurus bengalensis iriomotensis) is an endangered leopard cat that inhabits only Iriomotejima Island, Japan. The number of Iriomote cats is estimated to be approximately 100–110 and has been almost stable but slightly decreased in the coastal lowland. Infectious diseases are one of the major concerns in the conservation of Iriomote cats. Toxoplasma gondii is a protozoan parasite that causes toxoplasmosis. Toxoplasmosis is fatal in immunocompromised hosts, especially kittens and cat fetuses. We investigated the seroprevalence of T. gondii in Iriomote cats. Based on seroprevalence data, we simulated the effect of T. gondii infection on the population dynamics of Iriomote cats. The seroprevalence of T. gondii in Iriomote cats was significantly higher than that in domestic cats and dogs. Furthermore, the seroprevalence of T. gondii in domestic cats was significantly higher on Iriomotejima Island than on Okinawajima Island. Our simulation demonstrated that T. gondii eradication may help increase the population of Iriomote cats by an average of 11.5 (23.1%) cats in 2120. Therefore, controlling T. gondii may be an effective strategy for the conservation of Iriomote cats.