The distinct optical properties of surface-engineered quantum dots, featuring high fluorescent quantum yields and biocompatibility, render them valuable tools for precise and selective sensing and biosensing applications spanning diverse fields, including medicine, environmental monitoring, and diagnostics. In this study, we have successfully fabricated a new “OFF-ON” fluorescent probe based on 3-mercaptopropionic acid (MPA) - capped CdTe/ZnS QDs and neutral red (NR) for the determination of Naproxen (NAP) in pharmaceutical formulations and water samples. The as-prepared MPA-TGA-CdTe/ZnS QDs exhibit a robust photoluminescent emission, peaking at 544 nm upon excitation with a 380 nm wavelength. The quantum yield measurement for the TGA-CdTe QDs was ascertained to be 29.3 %. The findings displayed that the fluorescence emission of MPA-TGA-CdTe/ZnS quantum dots (QDs) could be significantly quenched by increasing neutral red concentration, which can be attributed to the formation of non-fluorescent NR- MPA-TGA-CdTe/ZnS QDs complex (NR-MPA energy level 1.15 Kcal/mol). Upon the addition of naproxen, there was a noticeable enhancement in fluorescence intensity because of the formation of the strong complex between naproxen and NR (NR-NAP energy level: −1.54 Kcal/mol), leading to the detachment of NR from the surface of quantum dots. Consequently, the MPA-TGA-CdTe/ZnS QDs became activated, resulting in the restoration of fluorescence intensity of MPA-TGA-CdTe/ZnS QDs. The enhancement of fluorescence intensity exhibited a direct relationship with the concentration of naproxen, following a linear trend within the concentration range of 2.00 × 10−1 to 27.3 µmol/L with the detection limits of 7.0 × 10−2 µmol/L. Moreover, computational studies were also used to validate the MPA-TGA-CdTe/ZnS QDs turn-off-ON sensor for sensing naproxen. The interactions of NAP, NR, and MPA-TGA-CdTe/ZnS QDs made a solid base for controlling the fluorescent reversibility of QDs. The as-prepared quantum dots were subjected to cytotoxicity studies using an MTT assay and AAS technique. These findings revealed that MPA-TGA-CdTe/ZnS QDs have greater biocompatibility and lower toxicity, making them attractive for biological applications. The recoveries of naproxen detection using the proposed fluorescent probe in various pharmaceutical formulations and water samples ranged from 97.4 % to 102 %, with a relative standard deviation of less than 5 %.