Background: Boron neutron capture therapy is a radiotherapy utilizing the neutron capture reaction. The commonly used boron agent, p-borono-l-phenylalanine (BPA), is accumulated in tumors by amino acid transporters upregulated in tumors. In this study, to propose a novel strategy of selective boron delivery targeting peptide transporter, we developed BPA-containing dipeptides (BPA-Tyr and Tyr-BPA) and examined their interaction with peptide transporters and their uptake into tumor cells. Methods: We established HEK293 cells stably expressing PEPT1 or PEPT2, and examined their interaction with BPA-Tyr and Tyr-BPA. Dipeptide transport activity was compared among tumors with varied PEPT1 and PEPT2 expression levels. We evaluated the boron accumulation in tumors after the treatment of BPA-Tyr and Tyr-BPA in vitro and in vivo. Results: BPA-Tyr and Tyr-BPA are transported by PEPT1 and PEPT2. The peptide transport activity in tumor cells correlated with PEPT1 expression level. BPA-Tyr and Tyr-BPA were delivered into PEPT1-expressing tumor cells via a PEPT1-mediated mechanism in vitro. In vivo, intravenous administration of BPA-Tyr resulted in a higher accumulation in the tumors compared with the blood. Conclusion: PEPT1 is a promising target for cancer-specific boron delivery in BNCT, using BPA-containing dipeptide-based boron agents.