Boron-dipyrromethene (BODIPY) dyes have received attention owing to their excellent photophysical properties, such as their biocompatibilities, photostability, thermal stability and propensities for synthetic modifications. In particular, meso -substituted BODIPY dyes have become the thrust of many current research reports, given that varying the meso -substituents enables tuning of the BODIPY scaffold's optical properties, especially by increasing Stokes shifts and redshifting emission wavelengths. Notably, the meso -substituents not only tune the dyes' photophysical properties but also serve as recognition sites, thereby retrofitting the meso -substituted BODIPY dye for the detection of bio-analytes. Hence, meso -substituted BODIPY dyes function as powerful design templates for fluorescence probes. This review summatively spans the past decade and highlights seven types of meso -substituted BODIPY dyes in addition to their spectral properties while emphasizing biomedical applications. • The optical properties of meso -substituted BODIPY are summarized. • The in vivo and in vitro biomedical sensing and imaging applications of meso -substituted BODIPY are outlined. • The challenges and perspectives of meso -BODIPY-based fluorescent probes are presented.