Korea Institute of Radiological and Medical Sciences provides proton irradiation service of up to 40 MeV using cyclotron. The use of such a cyclotron was approved in advance to satisfy the Nuclear Safety Act, and radiation safety was evaluated in this process. The Monte Carlo method is generally used to evaluate the shielding safety of high-energy accelerators, and MCNP 6.2 was used in the previous evaluation. In this study, in order to verify the results of previous evaluation, the calculation results of MCNP 6.2 and Particle and Heavy Ion Transport code System (PHITS) 3.24 are compared. PHITS is a general-purpose Monte Carlo particle transport simulation code that is used in many studies in the fields of accelerator technology, radiotherapy, space radiation, etc. In the previous evaluation, the effective dose by neutrons and photons generated by the collision of 40 MeV 20 μA of protons with a 10.5 mm thick beryllium target was evaluated, and in this study, this was reproduced with PHITS. As the radiation exposure evaluation for the user or pubic is evaluated based on the radiation dose and energy distribution generated around the target, the effective dose and energy distribution received by the water phantom with a radius of 1 cm on the front, side, and back of the target were calculated. T-Track, a tally of PHITS, was used to calculate effective dose, which is similar to F4 tally of MCNP 6.2 using a dose conversion factor. For the dose conversion factor, the value suggested as AP irradiation in Publication 103 was used. As a result of the calculation, the effective dose by neutrons at the front, side and back of the target was 1.42×105, 2.09×104, and 1.39×104 mSv·h−1, respectively, which was similar to 2.00×105, 1.84×104, and 2.59×104 calculated using F4 tally in MCNP. Moreover, the results of calculating the effective dose by photons using PHITS were 4.81×10, 3.10×10, and 2.66×10, respectively, and the results of calculating MCNP were 4.49×102, 6.45×10, and 9.64×10. The average energies of neutrons were 11.2, 0.69, and 0.31 MeV when calculated by PHITS, respectively, and 13.8, 7.8, and 4.6 when calculated by MCNP. Moreover, the average energies of photons were 1.98, 0.98, and 0.86 when calculated by PHITS, respectively, and 3.9, 3.2, and 2.6 when calculated by MCNP.