Peptide-based vaccines are relatively safe but have weak immune responses even with an adjuvant. In order to overcome the limitations of peptide-based vaccines, we developed peptide amphiphile (PA)-based nanofibers to enhance the immune responses for preventing enterovirus 71 (EV71) infectious disease (i.e., Hand, Foot, and Mouth Disease). PAs are peptides conjugated with fatty acid alkyl chain and able to self-assemble into various structures including high-aspectratio nanofibers. We designed PAs by coupling EV71 virus particle 1 (VP1) epitope peptides and spacer-crosslinker to the N-terminal of long-chain fatty acids (VP1-PA). PAs then self-assembled into nanofibers at physiological pH (pH 7.4). PA nanofibers were characterized by atomic force microscopy (AFM). For the immunization studies, C57BL/6 mice were injected intraperitoneally (i.p.) with recombinant VP1 with adjuvant (alum), VP1 epitope peptide with or without adjuvant, VP1-PA nanofibers with or without adjuvant, and PBS. To assess the immunogenecity of the VP1-PA nanofibers on serum samples from the immunized mice was analyzed by Western blot for the evaluation of VP1-specific IgG. The PA group showed a higher immune response than the peptide group. We expect that self-assembling VP1-PA based nanofibers as an immune stimulator could enhance immune responses effectively against EV71 infection and overcome the limitations of peptide-based vaccine.