Buckminsterfullerene C₆₀ is an emerging nanomaterial that has attracted interest for its diversity of potential applications. Since fullerene C₆₀ is only soluble in some organic solvents and is almost insoluble in water, recent efforts have been made to synthesize fullerene nanoparticles suspended in water suitable for use in aqueous and biological systems. Currently, there are two techniques employed to synthesize these nanoparticles. One technique involves first dissolving fullerene in an organic solvent before ultrasonicating the mixture in water to remove the organic solvent. Another technique simply requires the prolonged stirring of fullerene in water. Past studies have shown that fullerene nanoparticles synthesized through both techniques exhibit a negative electrophoretic mobility, the source of which is still unclear. In this study, we compare the electrokinetic properties and stability ratios of fullerene nanoparticles synthesized through both techniques with the objective of understanding the source of their surface charge. Electrophoretic mobility measurements showed that both nanoparticles remained negatively charged over the pH range of 2–12, and that the electrophoretic mobility became less negative towards the lower pH. The aggregation kinetics of these nanoparticles were derived through time-resolved dynamic light scattering over a range of sodium and calcium chloride concentrations. The nanoparticles synthesized through prolonged stirring proved to be more stable to aggregation than the other, implying that the synthesis technique plays an important influence over their surface characteristics. Spectroscopic study will be conducted to detect the formation of charged functional groups on the nanoparticles through the synthesis procedures.