In Brain cancer treatment by Proton Therapy the proper energy is calculated according to the volume, depth and place of tumor. One of the desired calculating methods is Monte Carlo Simulations and one of the popular codes which works with this method is MCNPX which is used in this thesis. At first the head of a mature patient has been simulated using Cylinder phantom made of water . A tumor with the radius of 2.54 cm has been simulated in the depth of 8.8 cm of brain and the patient's head is exposed to proton beams with energies from 110 MeV to 135 MeV with the steps of 1 MeV. Then graphs of proton and secondary neutrons doses-produced in brain- have been plotted. At the next stage the simulation is done for the same conditions by Snyder phantom. Then the results of proton therapy for two phantoms with different geometries and materials are compared. The comparison has shown that we gain two times greater TG when using Snyder phantom. Since Snyder phantom is much closer to the real geometry and components of the brain, this difference shows that using Cylinder phantom is not a good approximation in calculations in similar cases. Finally the optimum energy of proton beam for the most destruction of tumor and the least negative effect on the healthy tissue is determined between 130 MeV to 132 MeV. It is important to say that in this thesis dose of the produced secondary neutrons which are the sources of the secondary cancer is also calculated. The results of these calculations have shown that the secondary neutron dose in proton therapy is very small and it is about 0.01 of proton dose and this is one of the strength points of this treatment method. Finally by analyzing the results of proton therapy and BNCT(Boron Neutron Capture Therapy) it is shown that in proton therapy TG is greater and secondary neutrons dose is much less in comparison with BNCT.