The aim of this study is to understand the combined and differential biokinetic effects of radiofrequency (RF) electric-field hyperthermia as an adjunctive therapy to fullerene nanoparticle-based drug delivery systems in targeting the micro-vasculature and micro-environments of breast cancer tumors. Intravital microscopy (IVM) is an ideal tool to provide the spatial and temporal resolution needed for quantification in this investigation. The water-soluble and fluorescent fullerene derivative (C60-serPF) was designed to be an amphiphilic nanostructure, which is able to cross several biological membranes and accumulate in tumor tissues by passing through abnormally leaky tumor blood vessels. To elucidate the coupled effects of the highly permeable, but heterogeneous tumor vasculature, with the permeabilizing effects of mild (40–42 °C) hyperthermia produced by a local RF field, we controlled variables across tumor and non-tumor mammary gland microvasculature with and without application of RF hyperthermia in each condition. We notice that tumor tissue is characterized by more intense drug extravasation than in contralateral mammary fat pad tissue, which is consistent with enhanced permeability and retention (EPR) effects. The analysis of a permeability parameter (Papp), C60-serPF velocity, and the time of compound influx into the intra- and extra-vascular space suggest that mild RF hyperthermia can improve nanoparticle delivery into tumor tissue.