Background: in this study, two proton beam delivery designs, i.e. passive scattering proton therapy (PSPT) and pencil beam scanning (PBS), were quantitatively compared in terms of dosimetric indices. The GATE Monte Carlo (MC) particle transport code was used to simulate the proton beam system; and the developed simulation engines were benchmarked with respect to the experimental measurements. Method: a water phantom was used to simulate system energy parameters using a set of depth-dose data in the energy range of 120–235 MeV. To compare the performance of PSPT against PBS, multiple dosimetric parameters including Bragg peak width (BP W50), peak position, range, peak-to-entrance dose ratio, penumbra(90-10)%, penumbra(80-20)%, M 95% and dose volume histogram have been analyzed under the same conditions. Furthermore, the clinical test cases introduced by AAPM TG-119 were simulated in both beam delivery modes to compare the relevant clinical values obtained from Dose Volume Histogram (DVH) analysis. Results: the parametric comparison in the water phantom between the two techniques revealed that the value of peak-to-entrance dose ratio in PSPT is considerably higher than that from PBS by a factor of 8%. In addition, the BP_W50, penumbra(90-10)%, penumbra(80-20)%, and M 95% in PSPT was increased by a factor of 7, 51, 37, and 2.7%, respectively compared to the corresponding value obtained from PBS model. TG-119 phantom simulations showed that the difference of PTV mean dose between PBS and PSPT techniques are up to 1.8% while the difference of max dose to organ at risks (OARs) exceeds 50%. Conclusion: the results of this simulation show that although the passive scattering design method has a slightly higher ability to adjust the dose in target volume, but the active scanning proton therapy systems was superior in dose painting, and lower out-of-field dose compared to passive scattering design.