Decommission of medical cyclotron give rise to a lot of low-level radioactive waste and costs. Decommissioning cost should be reasonably calculated according to the decommissioning activities and installed components of facilities. In this paper, we investigated the experience on the cyclotron relocation from SNUH(Seoul National University Hospital) to SKKU(Sungkyunkwan University) and analyzed radioactive waste management costs by applying the disposal scenarios. Also considerations for decommissioning cost estimation are reviewed. The results could be utilized as a basic data for establishment on the methodology of decommissioning cost estimation and evaluation.