A neutron source from the C(d,n) reaction has the unique capability of producing medical radioisotopes such as Mo-99 with a minimum level of radioactive waste. Precise data on the neutron flux are crucial to determine the best conditions for obtaining the maximum yield of Mo-99. The measured yield of Mo-99 produced by the 100Mo(n,2n)Mo-99 reaction from a large sample mass of MoO3 agrees well with the numerical result estimated with the latest neutron data, which are a factor of two larger than the other existing data. This result establishes an important finding for the domestic production of Mo-99: approximately 50% of the demand for Mo-99 in Japan could be met using a 100 g (MoO3)-Mo-100 sample mass with a single accelerator of 40 MeV, 2mA deuteron beams.