The boron complexes of dipyrromethene (BODIPY®) comprise a class of fluorescent dyes that can be used in medical and biological studies. Fluorescent molecular labeling can be obtained by conjugation, or linking fluorescent dyes to certain proteins and peptides, in order to detect interactions, conformational changes and localization of specific peptides and parts of a protein. BODIPY molecules are relatively insensitive to the polarity and pH of their environment and are very stable to physiological conditions. The BODIPY core is strong enough to withstand a series of chemical reactions, and even the smallest changes to their structures enable the activation of their fluorescent properties. Herein, we have successfully synthesized N, N'-difluoroboryl-2,8-diethyl-1,3,7,9-tetramethyl-5-(4-isothiocyanatophenyl)-dipyrromethene, BODIPY derivative that is used for conjugation to proteins. Alternative pathway of synthesis is described with regard to literature. During the synthesis, a fluorescent group was lost in one step, however, desired BODIPY has been synthesized, thus possible pathways of synthesis in which fluorescent group can be preserved are discussed.