We recently developed a self-assembling peptide, E1Y9 (Ac-E-YEYKYEYKY-NH2), that forms supramolecular nanofibers with hydrogelation properties in response to Ca2+ ions. In this study, we proposed a new method to functionalize supramolecular peptide nanofibers using fiber-binding peptides screened from a phage peptide library. Three fiber-binding peptides, namely, p1, p2, and p3, were successfully identified. The RGDS-conjugated forms of these peptides, namely, p1-RGDS, p2-RGDS, and p3-RGDS, significantly enhanced the adhesion of 3T3-L1 cells on E1Y9 nanofibers through noncovalent modification of E1Y9 nanofibers. This noncovalent modification using fiber-binding peptides was also effective for functionalization of E1Y9 hydrogels, as E1Y9 hydrogels modified with p1-RGDS or p2-RGDS promoted the proliferation of 3T3-L1 cells, compared with the E1Y9 hydrogel alone. Since p1 and p2 could bind to different sites on E1Y9 nanofibers, the additional enhancement in cell proliferation on E1Y9 hydrogels was achieved using both p1-RGDS and p2-RGDS. Thus, the functionalization of supramolecular peptide nanofibers using molecular recognition peptides will be a powerful tool for the development of functional materials. We proposed a new method to functionalize supramolecular peptide nanofibers using fiber-binding peptides screened from a phage peptide library. The RGDS-conjugated fiber-binding peptides significantly enhanced the adhesion of 3T3-L1 cells on E1Y9 nanofibers through noncovalent modification of E1Y9 nanofibers. This noncovalent modification using fiber-binding peptides was also effective for functionalization of E1Y9 hydrogels as cell culture materials that promoted the proliferation of 3T3-L1 cells. The functionalization of supramolecular peptide nanofibers using molecular recognition peptides will be a powerful tool for the development of functional materials.