A set of BODIPY‐carboranyl dyads synthesized by a Sonogashira cross‐coupling reaction, where different C‐substituted ortho‐ and meta‐carboranyl fragments have been linked to a BODIPY fluorophore is described. Chemical, photophysical and physicochemical analyses are presented, including NMR and single XRD experiments, optical absorption/emission studies and partition coefficient (log P) measurements. These studies, supported by DFT computations (M06‐2X/6‐31G**), provide an explanation to the largely divergent cell income that these fluorescent carboranyl‐based fluorophores display, for which a structural or physicochemical explanation remains elusive. By studying the cell uptake efficiency and subcellular localization for our set of dyads on living HeLa cells, we tracked the origins of these differences to significant variations in their static dipole moments and partition coefficients, which tune their ability to interact with lipophilic microenvironments in cells. Remarkably, m‐carboranyl‐BODIPY derivatives with a higher lipophilicity are much better internalised by cells than their homologous with o‐carborane, suggesting that m‐isomers are potentially better theranostic agents for in vitro bioimaging and boron carriers for boron neutron capture therapy.