Currently, international nuclear fission reactors producing medical isotopes face the problem of shutdown and maintenance, decommissioning, or dismantling, while the production capacity of domestic research reactors for medical radioisotopes is inadequate, and the supply capacity for medical radioisotopes faces major challenges in the future. Fusion reactors are characterized by high neutron energy, high flux density, and the absence of highly radioactive fission fragments. Additionally, compared to fission reactors, the reactivity of the fusion reactor core is not significantly affected by the target material. By building a preliminary model of the China Fusion Engineering Test Reactor (CFETR), a Monte Carlo simulation was performed for particle transport between different target materials at a fusion power of 2 GW. The yields (specific activity) of six medical radioisotopes (14C, 89Sr, 32P, 64Cu, 67Cu, and 99Mo) with various irradiation positions, different target materials, and different irradiation times were studied, and compared with those of other high-flux engineering test reactors (HFETR) and the China Experimental Fast Reactor (CEFR). The results show that this approach not only provides competitive medical isotope yield, but also contributes to the performance of the fusion reactor itself, e.g., tritium self-sustainability and shielding performance.