Regioselective and stepwise syntheses of a series of functionalized BODIPY dyes through palladium-catalyzed cross-coupling reactions and direct C-H arylations have been developed. In particular, this method allows the straightforward synthesis of 2,6-dibromo-3,5-diarylBODIPYs and 2-bromo-3-arylBODIPYs from polybrominated BODIPYs. The X-ray structure of intermediates 5a-c indicated that the palladium was first inserted into the C-Br bonds at 3,5-positions of brominated BODIPYs. The resulting 2,6-dibromo-substituted BODIPYs are potential long wavelength photosensitizers which are not easily accessible using previous methods.