The present paper describes the validation of the new decay heat evaluation method using the FPGS90 code with updated nuclear data library such as JENDL-4.0 library, by comparing with the results of the decay heat measurement of the two spent MOX fuel subassemblies in the Japanese experimental fast reactor Joyo MK-II core and by comparing with the calculation results of the similar calculation code ORIGEN2.2. The rational extent of uncertainty of the decay heat evaluation method was installed. The measured decay heat of the subassemblies ranged from 1445±24W to 158±9W in between 40 and 729 days of the cooling time. The calculated values of decay heat (C) by FPGS90 based on the JENDL-4.0 library were coincident with the measured ones (E) within the calculation uncertainties, and the C/E values ranged from 1.01 to 0.93. FPGS90 evaluated the decay heat almost 3% larger than OR-IGEN2.2, and it improved the C/E of decay heat in comparison with ORIGEN2.2. Furthermore, the C/E of decay heat by FPGS90 based on the JENDL-4.0 library was improved than that based on the JENDL-3.2 library, and the contribution of the revision of cross section library to the improvement was dominant rather than that of the decay data and fission yield data libraries.