EphA4 is a member of the Eph family of receptor tyrosine kinases and has important functions in the developing and adult nervous system. In the adult, EphA4 is enriched in the hippocampus and cortex, two brain structures critical for learning and memory. To identify reagents that can discriminate between the many Eph receptors and selectively target EphA4, we used a phage display approach. We identified three 12-amino acid peptides that preferentially bind to EphA4. Despite lack of a common sequence motif, these peptides compete with each other for binding to EphA4 and antagonize ephrin binding and EphA4 activation at micromolar concentrations, indicating that they bind with high affinity to the ephrin-binding site. Furthermore, one of the peptides perturbs the segmental migration of EphA4-positive neural crest cells in chick trunk organotypic explants. Hence, this peptide can disrupt the physiological function of endogenous EphA4 in situ. We also identified additional peptides that bind to EphA5 and EphA7, two other receptors expressed in the nervous system. This panel of peptides may lead to the development of pharmaceuticals that differentially target Eph receptors to modulate neuronal function in specific regions of the nervous system.