Anionic boron clusters, such as [B12X12]2− (X = Cl, Br, I), have attracted attention in pharmaceuticals due to their unique superchaotropic properties. In particular, [B12Br12]2− (1) has demonstrated strong interactions with biomolecules, facilitating cargo translocation across plasma membranes. In this study, we investigated the effect of covalently attaching chlorinated dodecaborate moiety [B12Cl11O-]2− to 6-carboxyfluorescein (6-FAM) (3) via a PEG3 linker to form conjugate (4). We compared the membrane permeability of this covalent conjugate with that of non-covalent interactions between 6-FAM (3) and [B12Cl12]2− (2). Live-cell fluorescence imaging revealed that the covalent conjugate exhibited enhanced membrane permeability and water solubility while maintaining low cytotoxicity. These results highlight the potential of covalent conjugation with boron clusters for improving the cellular uptake of hydrophilic cargos.