In this study, we have designed and synthesized a new near-infrared (NIR) fluorescent probe (BODIPY-Se) to detect fluorine ions (F-) using a B-Se bond to connect the fluorescent dye BODIPY and benzotrifluoride. The probe exhibited a highly selective fluorescence response to F- with a detection limit of 7.4×108 mol/L. The excitation and emission spectra of the probe in the NIR region avoid background fluorescence interference present in biological systems. The fluorescent imaging of HepG2 cells demonstrated that the newly developed probe should be broadly applicable to detect F- in living cells.