A new tripod boron dipyrromethene (BODIPY) dye bearing N-tert-butoxycarbonyl (N-Boc) amine side chain was synthesized and the functionality was confirmed by means of its acetylation reaction with acetic anhydride. Deprotection of the N-Boc protective group had been successfully performed using boron trifluoride etherate (BF3·OEt2) solution alone or the combination of BF3·OEt2 and molecular sieves to solve the susceptibility of the BODIPY fluorophore under the protonic acid conditions. All the new structures had been characterized by NMR, HRMS and IR spectra. A conformational isomeric phenomenon was observed originating from partly restricted rotation of the RNH group attached to the 1,3,5-triazine ring. This work made the chemical transformation via amine functionality around meso position in the tripod BODIPY available.