Three acidotropic, near-infrared fluorescent probes based on piperazine-modified BODIPY dyes (A, B and C) have been developed for the sensitive and selective detection of lysosomal pH in living cells. Probes A and B display low solubilities in aqueous solutions, whereas probe C is highly water-soluble. The fluorescent responsive mechanism of these probes to lysosomal pH is based on intramolecular charge transfer (ICT) and potential photo-induced electron transfer from piperazine moieties at 3,5-positions to BODIPY cores in the near-infrared region. The sensitivity and selectivity of the probes to pH over metal ions have been investigated by spectroscopic analysis in aqueous solutions. The probes have low auto-fluorescence at physiological pH conditions, whereas their fluorescence intensities significantly increase when pH is shifted to an acidic condition. Furthermore, these three probes were successfully applied to the in vitro lysosome imaging inside normal endothelial and breast cancer cells.