A general and efficient method for α-chlorination of 4,4'-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) has been developed using CuCl2 as chlorination reagent. The reaction is characterized by complete 3/5-positions of BODIPY regioselectivity. This unusual highly regioselective α-halogenation of BODIPY is in sharp contrast to previously reported halogenation methods which preferred to occur first at the 2,6-positions of BODIPY. This approach provides a straightforward, facile, and economical route to 3- and/or 5-chloroBODIPYs with various meso-groups (H, alkyl, and aryl) and their derivatives.