In this study, we describe the fabrication of novel fullerene-containing peptide-nanoparticles through self-assembly. A water-soluble, poly(l-glutamic acid)-attached fullerene was newly synthesized and the conformation and self-assembling property in water were examined by using circular dichroism, FTIR, UV, atomic force microscopy, and dynamic light scattering measurements. In the lower pH region (<6.8), the fullerene peptide self-assembles into nanoparticles that are ca. 100–200 nm in diameter. These nanoparticles are rich in α-helices, and stacking interaction of fullerene moieties contributes to the stability of the high-order structure. In addition, these particle sizes can be easily controlled by changing pH that results in causing the conformational transition of PLGA segment. Finally, the fullerene-containing nanoparticle is confirmed to be capable of removing the biologically important superoxide radical in comparison with the superoxide dismutase.