Carbon-shelled, iron-based magnetic nanoparticles (C/Fe MNPs) were found to act as strong heat generating agents when exposed to radio-frequency (RF) energy with the ability to thermally destroy cancer cells. In order to efficiently deliver MNPs to cancer cells and to enhance the effectiveness of the RF treatment, human epidermal growth factor (EGF) was bioconjugated with the C/Fe MNPs for their specific delivery to two cancer cell lines, MCF-7 breast cancer cells and Panc-1 pancreatic cancer cells, respectively. These cell lines overexpress the epidermal growth factor receptors (EGFRs) and were used in this study as models. EGF-MNPs have shown higher surface binding efficiency towards the MCF-7 cells based on the comparative ζ-potential measurements. Confocal optical microscopy further confirmed that EGF-bioconjugated MNPs highly accumulated around and inside of these cancer cells. RF treatment was found to destroy 92.8% of MCF-7 breast cancer cells during 10 minutes of treatment when EGF was bound to the nanoparticles, while 37.3% of cells died when MNPs alone were used in identical conditions. Panc-1 cancer cells exhibit a higher resistance than MCF-7 cells when they were exposed to MNPs or RF treatment. Cytotoxicity studies demonstrated that the EGF-C/Fe MNP bioconjugates present lower toxicity compared to the C/Fe MNP. Caspase assay studies demonstrated that the MCF-7 cancer cells underwent an apoptotic process by the caspase 3 deficiency pathway showing no evidence of morphological changes such as membrane blebbing.