A novel fluorenone-naphthyl pendant sensor (FTU) possessing thiourea functionality has been synthesized via a simple condensation method and utilized for the recognition of F− and Hg2+ ions in the solution of CH3CN. The addition of F− and Hg2+ ions to the FTU solution led to the appearance of red-shifted absorption bands at 340 and 315 nm, respectively. On the other hand, in the fluorescence spectrum, the two-fold decrease in fluorescence intensity of probe FTU was observed with F− ions; while complete quenching of the fluorescence intensity was noticed with Hg2+ ions at 423 nm. The limit of detection values of F− and Hg2+ ions were found to be 1.02 & 29.1 nM, respectively, measured by UV–vis studies and 0.0185 & 0.81 nM, respectively, measured by fluorescence studies, which are less than recommended by WHO. DFT computational assessments and 1H NMR titration experiments pointed to F− induced deprotonation of thiourea NH signals. However, the chelation-enhanced quenching effect (CHEQ) was held responsible for fluorescence quenching with Hg2+ addition. Moreover, the in-situ formed FTU + F− complex was utilized for secondary sensing of drug sobisis. Furthermore, the real-world applicability of sensor FTU has been successfully scrutinized for the recognition of F− ions in the toothpaste samples. In addition, molecular docking studies revealed that FTU exhibited excellent antibacterial potency towards different gram-positive as well as negative strains.