We have been developed an epithermal neutron source for boron neutron capture therapy(BNCT), consisting of a cyclotron accelerator that can provide a - 1 mA, 30 MeV proton beam, a neutron production beryllium target and the moderator that can reduce the energy of fast neutrons to an effective energy range. In order to validate the simulations, we measured the depth distribution of the thermal neutron flux in water phantom located at the treatment position. The measured results were compared with the simulations using the MCNPX Monte Carlo code. The good agreement between the simulations and measurements was shown. The thermal neutron flux with the proton current of 430 μA was 7.4 × 108 (neutrons cm-2 s-1) at the depth of around 20 mm in the water phantom. This intensity corresponds to the neutron source of Kyoto University Research Reactor (KUR), at which 275 clinical trials of BNCT have been performed. We experimentally confirmed that our cyclotron based neutron source can use for clinical trials of BNCT. ©2009 IEEE.