Flagellin activates innate, cellular and humoral immunity through Toll-like receptor 5 (TLR5), and this interaction can be exploited to improve vaccines against oncogenic human papillomavirus (HPV). The binding mechanism between flagellin-fabricated peptide vaccines (FFPVs) and TLR5, however, remains unclear. Here, three FFPV candidates (C58, C52 and C16) were designed from overlapped epitope segments in the conserved N-terminal region of the L2 minor capsid protein of HPV58, HPV52 and HPV16. These segments were predicted to induce cytotoxic T-lymphocyte, T-helper, IFNγ and B-cell responses. Each construct also carried two TLR agonist adjuvants (flagellin and RS09), two universal T-helper epitopes and defined peptide linkers. Physicochemical and immunological properties were evaluated, and three-dimensional models of the FFPVs and TLR5 were generated, refined and validated. Protein–protein docking with HADDOCK and PRODIGY ranked the TLR5-C58 complex highest, ahead of TLR5-C16 and TLR5-C52. To test the docking result, the TLR5-C58 complex was simulated for [100 ns] in explicit solvent, and the root mean square deviation, total energy, hydrogen bonds and key-residue distances were analyzed. The simulation identified a binding mode with ten key residues in the leucine-rich repeat (LRR) region of TLR5, and the binding free energies agreed with experimental reports. These findings offer a structural basis for the rational design of L2-based vaccines against cervical cancer.