This work evaluated the validity of computer simulation codes by comparing the results of an inventory calculation for a89Zr target assembly with measured data obtained using a high-purity germanium detector. For the inventory calculation, the MCNP6 and FISAPCT-Ⅱ codes were used, and for the measurement, efficiency derived from the efficiency transfer method was used. The MCNP6's ENDF/B-Ⅶ library (TENDL-2017 library for 89Y) and the CEM03.03 physics model were employed to simulate proton reactions, while the ENDF/B-Ⅶ library alone was utilized for neutron reactions. To verify the efficiency obtained by the efficiency transfer method, the calculated activity of the reference sources was compared with the measured activity and confirmed to be within 11%. For the target assembly, the average calculated-to-measured activity (C/M) ratio was determined to be 0.7–2.0 (physics model) and 0.7–1.5 (data library with TENDL), thus confirming the validity of the computer simulation codes. The above results suggest that the methods presented in this study could be used to establish decommissioning plans for the cyclotron facility, including plans for waste disposal of cyclotron components such as target assemblies.