The molecular engineering of boron dipyrromethenes (BODIPYs) has garnered widespread attention due to their structural diversity enabling tailored physicochemical properties for optimal applications. However, catalytic enantioselective synthesis of structurally diverse boron‐stereogenic BODIPYs through intermolecular desymmetrization and BODIPYs with atroposelectivity remains elusive. Here, we showcase rhodium(II)‐catalyzed site‐specific C‐H (hetero)arylations of prochiral BODIPYs and polysubstituted BODIPYs with diazonaphthoquinonesand diazoindenines, providing efficient pathways for the rapid assembly of versatile (hetero)arylated boron‐stereogenic and axially chiral BODIPYs through long‐range desymmetrization and axial rotational restriction modes. The synthetic application of the procedures has been emphasized by the efficient synthesis of BODIPY derivatives with various functions. Photophysical properties, bioimaging, and lipid droplet‐specific targeting capability of tailored BODIPYs are also demonstrated, indicating their promising applications in biomedical research, medicinal chemistry, and material science.