β-MoO3 whiskers prepared by a thermal evaporation method and α-MoO3 particles were irradiated in a nuclear reactor to produce 99Mo/99mTc radioisotopes via neutron capture. The irradiated targets were then dispersed in water to extract the 99Mo/99mTc isotopes. Of the 99Mo formed in the β-MoO3 whiskers, 64.0 ± 7.4% was extracted with water; by contrast, only 8.8 ± 2.6% of the 99Mo formed in α-MoO3 was extracted. By comparing these data to the 98Mo concentration dissolved in water, we confirmed the hot-atom effect on both β-MoO3 whisker and α-MoO3 particle targets to transfer 99Mo isotopes from irradiated samples to water. In addition, the β-MoO3 whiskers exhibited a prominent hot-atom effect to transfer a higher ratio of 99Mo isotopes into water. To the best of our knowledge, this research is the first demonstration of β-MoO3 being used as an irradiation target in the neutron capture method. On the basis of the results, β-MoO3 is considered a promising irradiation target for producing 99Mo/99mTc by neutron capture and using water for the radioisotope extraction process in the future.