The aim of this study was to create molecularly imprinted polymers (MIPs) that are specific towards 4-borono-L-phenylalanine (BPA) to serve as boron compound carriers. The honeycomb-like MIPs were characterized in the matter of adsorption properties, morphology, structure, and cytotoxicity towards A549 and V79-4 cell lines. The honeycomb-like MIP composed from methacrylic acid and ethylene glycol dimethacrylate was characterized by a binding capacity of 330.4 ± 4.6 ng g−1 and an imprinting factor of 2.04, and its ordered, porous morphology was confirmed with scanning electron microscopy. The theoretical analysis revealed that the coexistence of different anionic forms of the analyte in basic solution might lower the binding capacity of the MIP towards BPA. The release profiles from the model phosphate buffer saline showed that only 0 to 4.81% of BPA was released from the MIP within the time frame of two hours, furthermore, the obtained material was considered non-cytotoxic towards tested cell lines. The results prove that MIPs can be considered as effective BPA delivery systems for biomedical applications and should be investigated in further studies.