Recently, magnetic nanoparticles (MNPs) based hyperthermia therapy has gained much attention due to its therapeutic potential in biomedical applications. This necessitates the development of numerical models that can reliably predict the temporal and spatial changes of temperature during the therapy. The objective of this study is to develop a comprehensive numerical model for quantitatively estimating temperature distribution in the ferrofluid system. The reliability of the numerical model was validated by comparative analysis of temperature distribution between experimental measurements and numerical analysis based on finite element method. Our analysis showed that appropriate incorporation of the heat effects of electromagnetic energy dissipation as well as thermal radiation from the ferrofluid system to the surrounding in the modeling resulted in the estimation of temperature distribution that is in close agreement with the experimental results. In summary, our developed numerical model is useful to evaluate the thermal behavior of the ferrofluid system during the process of magnetic fluid hyperthermia.