Aptides is a novel class of high-affinity peptides that recognize diverse molecular targets with high affinity and specificity. Here we report the solution structure of an aptide APT specifically bound to fibronectin extradomain B (EDB), a prominent marker of tumor angiogenesis. The complex structure reveals an unusual protein-protein interaction via coupled unfolding and binding. APT binding is accompanied by unfolding of the C-terminal β strand of EDB, permitting APT to interact with fresh-exposed hydrophobic interior surfaces of EDB. The β-hairpin scaffold of APT drives the interaction by a β-strand displacement mechanism, such that an intramolecular β sheet is replaced by an intermolecular β sheet. Unfolding of EDB perturbs the tight domain association between EDB and FN8 of fibronectin, highlighting its potential use as a scaffold that switches between stretched and bent conformations.