The objective is to validate a designed heating protocol in a previous study based on treatment efficacy of magnetic nanoparticle hyperthermia in prostate tumors. In vivo experiments have been performed to induce temperature elevations in implanted PC3 tumors injected with magnetic nanoparticles, following the same heating protocol designed in our previous microCT-based theoretical simulation. A tumor shrinkage study and histological analyses of tumor cell death are conducted after the heating. Tumor shrinkage is observed over a long period of 8 weeks. Histological analyses of the tumors after heating are used to evaluate whether irreversible thermal damage occurs in the entire tumor region. It has been shown that the designed 25 min heating (Arrhenius integral Ω ≥ 4 in the entire tumor) on tumor tissue is effective to cause irreversible thermal damage to PC3 tumors, while reducing the heating time to 12 min (Ω ≥ 1 in the entire tumor) results in an initial shrinkage, however, later tumor recurrence. The treated tumors with 25 min of heating disappear after only a few days. On the other hand, the tumors in the control group without heating show approximately an increase of more than 700% in volume over the 8-week observation period. In the undertreated group with 12 min of heating, its growth rate is smaller than that in the control group. In addition, results of the histological analysis suggest vast regions of apoptotic and necrotic cells, consistent with the regions of significant temperature elevations. In conclusion, this study demonstrates the importance of imaging-based design for individualized treatment planning. The success of the designed heating protocol for completely damaging PC3 tumors validates the theoretical models used in planning heating treatment in magnetic nanoparticle hyperthermia.