One of the most significant challenges in boron neutron capture therapy (BNCT) is to have an ideal boron delivery agent which can deliver sufficient numbers of boron atoms to designated tumor cells. In this work, mild synthetic conditions for synthesis of dipeptidyl multiple boron-containing analogs under microwave-assisted condition were investigated. The results showed that the reaction generally took place at 50 °C, but higher reaction temperature was required when a fluorinated building block was used. The resulting peptidyl skeletons generated by Ugi four-component reaction resemble basic cell metabolites and could potentially be used as alternative replacements for current boron carrier agents in BNCT.