For producing radionuclides which were mostly used in medical purposes, for instance, Positron Emission Tomography (PET), there were about 1,200 PET cyclotrons operated in 95 countries based upon IAEA database (2020). Besides, including PET cyclotrons, demands for particle accelerators are continuously increasing. In Korea, about 40 PET cyclotrons are in operating phases (2020). Considering design lifetime (about 30–40 years) of cyclotrons, there will be demands for decommissioning cyclotron facilities in the near future. PET cyclotron produces radionuclides by irradiating charged particles to the targets. During this phase, nuclear reactions (18O(p,n)18F, 14N(d,n)15O etc.) produce secondary neutrons which induce neutron activation of accelerator itself as well as surrounding infrastructures (the ancillary subsystems, peripheral equipment, concrete walls etc.). Most of the ancillary systems including peripheral equipment can be neutron activated, since, most of them were made of steels. Steels like stainless steel or carbon steel may contain some impurities, typically cobalt. Although, there were several researches evaluating activation of concrete walls and accelerator components, estimating the activation and influence on neutron interaction of the other surrounding infrastructures were insufficient. In this study, by using computational neutron transport code (MCNP 6.2), and source term calculation code (FISPACT- II), we estimated neutron distribution in cyclotron vault and activation of ancillary subsystems including some peripheral equipment. Also, using Au foil and Cd cover, we measured thermal neutron distribution at 16 points on the concrete wall, and compared it to calculated results (MCNP). Even though, the compared results matches well, there was a discrepancy of neutron distributions between presence and absence of those equipment. Additionally, in estimating activation distributions by calculating, most of the steel-based subsystems including peripheral equipment should be managed by radioactive wastes after 20 years of operation. Throughout this study, we could find that influence on neutron interaction of those equipment can affect neutron distribution in concrete walls. This results vary the activation depth as well as location of the hot contaminated spot in concrete wall. For estimating or evaluating activation distributions in cyclotron facilities, there was need to consider some equipment located in cyclotron vault.