Nanoscale aggregation of a new methanofullerene derivative with peripheral hydrophilic moieties was achieved within the confined space of a Nafion membrane. Transmission electron microscopic examination revealed an average size of 5.0 nm for the aggregates, while optical, fluorescence, and X-ray photoelectron spectroscopic measurements indicated excimer formation within the well-defined aggregated structure. These nanocomposites based on fullerene derivatives exhibit a significant optical-limiting capability attractive for many potential applications.