Neutron yields from 9Be(p,xn) reactions with a 2-cm thick beryllium target bombarded by proton beams of 5, 6, 7, 8, 9, and 10 MeV were investigated. Neutron beam characteristics through a pilot design of beam shaping assembly were calculated by using MCNP6, PHITS, and GEANT4. The neutron yield with a 10 MeV beam by MCNP6 was 7.7 times larger than values by the other codes, but close to the experimental data. The neutron spectrum and directionality were different among the codes. These differences could stem from different cross-section libraries and models used in the codes. The epithermal flux at the beam irradiation port by MCNP6 was 1.4 × 109 cm−2 s−1 for a proton current of 8 mA hitting the target. The ratio of thermal and epithermal flux was less than 0.01 and the forward directionality was 0.78. However, we suggest a new criterion regarding a ratio of fast and epithermal flux.