A novel probe incorporating quaternized 4-pyridinium group into a BODIPY molecule was synthesized and studied for the selective detection of fluoride ions (F^-) in aqueous solution. The design was based on a fluoride-specific desilylation reaction and the “Turn-On” fluorescent response of probe 1 to F^- was ascribed to the inhibition of photoinduced electron transfer (PET) process. The probe displayed many desired properties such as high specificity, appreciable solubility, desirable response time and low toxicity to mammalian cells. There was a good linearity between the fluorescence intensity and the concentrations of F^- in the range of 0.1–1 mM with a detection limit of 0.02 mM. The sensing mechanism was confirmed by the NMR, electrospray ionization mass spectrum, optical spectroscopy and the mechanism of “Turn-On” fluorescent response was also determinated by a density functional theory (DFT) calculation using Gaussian 03 program. Moreover, the probe was successfully applied for the fluorescence imaging of F^- in human epithelial lung cancer (A549) cells and alveolar type II (ATII) cells under physiological conditions.