In worldwide, tens of thousands of units of particle accelerators have been used and more than 97% of those accelerators are used for dedicated medical of commercial applications. Radionuclide production cyclotron produce several positron-emitting radionuclides such as 18F by 18O(p,n)18F reaction which generates secondary neutrons. It is of note that these neutrons cause neutron activation in structures and components of cyclotron facilities. Therefore, International Atomic Energy Agency had addressed that a well-developed estimate of the neutron activation induced radioactive inventory of accelerator facilities is needed for the proper planning and safe implementation of decommissioning using proven methods or codes that can be used to perform activation calculations. Moreover, IAEA suggested that during the operation of cyclotrons, concrete walls become radioactive over time and this radioactivity needs to be fully characterized as part of early decommissioning planning. In this study, Neutron activation in the medical cyclotron facilities was evaluated with the MCNP and FISPACT-II code to analyze the generation of decommissioning radioactive wastes during facilities dismantling. For the reference case, residual radioactivity concentration of each activation product (e.g. 60Co, 152Eu, etc.) was calculated and the sum of fractions of the activity concentration of each radionuclide divided by its clearance level was exceeded 1.0 at each calculation point which means radioactive waste generations during decommissioning of the facility. Several points show the calculated sum of fractions (SoF) at inside wall were bigger than the surface wall. The reason of these phenomena is that the slowdown of the incident neutron energy at the inside wall due to neutron attenuation and larger thermal neutron flux than surface wall. It is of note that each activation reaction cross-section was dominant at thermal neutron energy band. Sensitivity analysis was conducted to analyze the effects of design characteristics (e.g. beam energy and current, operation period, and workload). The SoF was exceeded 1.0 at the least activation condition (i.e. 9 MeV, 10 μA) if the operation period was 10 years. For the realistic condition such as 13 MeV, only 10 μA of beam current case shows the SoF was under union. On the other hand, 19 MeV, 60 μA, and 10 years operation case shows the SoF as 20.4 which means the clearance rule can be applied only after 21 years of decay-in-storage. The result of this study can be used for proper planning of decommissioning and/or new installation of cyclotron facilities include considerations of radioactive waste management.