A new boron–dipyrromethene-based lysosome tracker, Lyso-NIR, is facilely synthesized. Besides the intensive near-infrared (NIR) fluorescence and high photostability, Lyso-NIR shows the capability to stably localize in lysosomes, which is independent of the local pH. Lyso-NIR does not have the problematic alkalization effect suffered by the commonly used lysotrackers; thus, it shows ignorable cytotoxicity and slightly affects normal physiological functions of lysosomes. The above advantages of Lyso-NIR make it feasible to track lysosomes’ dynamic changes in a relatively long time during the full cellular processes such as apoptosis, heavy metal stimulation, and endocytosis, as is demonstrated in this work. Moreover, Lyso-NIR’s narrow NIR emission at 740 nm with a full width at half-maximum smaller than 50 nm makes it easy to avoid the crosstalk with the emissions from other common fluorescent probes, which strengthens Lyso-NIR’s competitiveness as a standard lysosome tracker for multicolor bioimaging.Keywords: fluorescence imaging; lysosome; near-infrared; probe