Abstract. The dose distributions from proton pencil beam scanning were calculated by FLUKA, GEANT4, MCNP, and PHITS, in order to investigate their applicability in proton radiotherapy. The first studied case was the integrated depth dose curves (IDDCs), respectively from a 100 and a 226-MeV proton pencil beam impinging a water phantom. The calculated IDDCs agree with each other as long as each code employs 75 eV for the ionization potential of water. The second case considered a similar condition of the first case but with proton energies in a Gaussian distribution. The comparison to the measurement indicates the inter-code differences might not only due to different stopping power but also the nuclear physics models. How the physics parameter setting affect the computation time was also discussed. In the third case, the applicability of each code for pencil beam scanning was confirmed by delivering a uniform volumetric dose distribution based on the treatment plan, and the results showed general agreement between each codes, the treatment plan, and the measurement, except that some deviations were found in the penumbra region. This study has demonstrated that the selected codes are all capable of performing dose calculations for therapeutic scanning proton beams with proper physics settings.