Nowadays, cancer is one of the most important concerns in human being's societies, more than one-third of people in around the world will get cancer during their lives. At present, approximately 14 million people in the world are living with cancer. Various treatment approaches have been used to treat tumors of brain among which radiation therapy, especially proton therapy, has been of utmost importance because of its special benefits. Physical dose depth distribution characteristic of protons in a tissue is determined with a low dose in the entrance region, maximum dose in the Bragg region, and rapid decline takes place near the end of their range. The ability to treat internal tumors, the ability of the broadening of the Bragg peak, and the small size of the particles are the other advantages of this approach which cause less damage to healthy tissues surrounding the tumor as compared to other therapy approaches such as radiation therapy with X-ray. At present, fast algorithm is generally used to obtain treatment plan (dose distribution in the patient). This means that at first absorbed dose in water phantom is calculated and then the necessary changes on the beam, equipment and location of the patient are applied, but this approach does not consider the dose resulting from radioactive decay in the tissue. Although radioactive products such as 3 H(T 1/2 =12/32 a), 7 Be(T 1/2 =53/3 d), 14 C(T 1/2 =5730 a), and 22 Na(T 1/2 =2/6 a) which are produced by interaction between protons and tissues' constituent elements have high longevity, they are produced in small quantities, but nuclei that decay to the ground state with positron emission and have low longevity time such as 11 C(T 1/2 =20.3 min), 13 N(T 1/2 =9.96 min), and 15 O(T 1/2 =2.03 min) are produced in amount that calculation of their dose is an integral part of plan treatment. These nuclei are more produced during following interaction mechanisms: 12 C(p,pn) 11 C, 14 N(p,x) 11 C, 16 O(p,x) 11 C, 12 C(p,?) 13 N, 14 N(p,pn) 13 N, 16 O(p,x) 13 N, 14 N(p,n) 15 O, and 16 O(p,pn) 15 O. These short-longevity radioactive products reach their maximum amount along the proton path and particularly in Bragg region. In addition, a portion of produced photons from the annihilation of positronium atoms are absorbed by tissues and may cause unwanted dose to be applied to the surrounding treated tissues. Although, their produced dose is low, but they are not negligible and their amount should be calculated on the treatment plan. In this study, absorbed dose of protons and secondary particles such as neutrons and positrons in a head phantom have been calculated using the MCNPX 2.6 simulation code. At first, the rate of the production of positron-emitter elements in different interactions have been studied. Then, proton therapy devices such as Wobbler, scatterer, ridge filter, and collimator have been designed for water phantom and after that the rate of the dose of protons, neutrons and positrons for the MIRD phantom with a tumor with radius 3cm located in its center has been calculated by code MCNPX. In addition, a portion of the photons from the annihilation of positronium atoms are absorbed in tissue, and may cause unwanted dose be applied to the surrounding parts of the treated tissue, although, the produced dose is low, it is not negligible and its value should be calculated on the treatment plan. The results indicate that for protons with 190 MeV energy, 85.8%, 24.3%, 4.13% and 24.7% of the total dose had reached to the tumor, brain, bone, and skin, respectively, had been the result of secondary particles investigated in this research. Also for protons with 150 MeV energy, 9.1%, 22.8%, 44.6%, and 47.5% of the total dose reached to the tumor, brain, bone, and skin, respectively, had been the result of the sum of the protons, neutrons, positrons and photons dose resulting from the annihilation of positronium atoms.