Nanostructured molecular imprinted polymer for the sensitive and selective fluorometric detection of Cephalexin has been developed using a core-shell imprinting technology. The polymer coat on silica nanoparticles acquires a large surface area to adsorb the analytes. A hydrophilic functional monomer N-[Tris(hydroxymethyl)methyl]acrylamide and crosslinker ethylene glycol dimethylacrylate were used to synthesize the imprinted polymer to enhance the water dispersibility. The imprinted polymer was characterized with FTIR, FESEM and HRTEM. The diameter of the imprinted polymer appears to be ∼200–500 nm size. An environment-sensitive coumarin-based fluorescent monomer was integrated into the polymer as a signaling unit. The polymer shows a turn-on emission behaviour upon adsorption of Cephalexin on the surface. The limit of detection of Cephalexin is 1.6 μM. The imprinted polymer efficiently detects the drug molecule in synthetic urine samples also. The interaction of the monomer and the drug molecules was further supported with the optimized geometries, electron density calculation at the hydrogen bond critical points, and reduced density gradient (RDG) analysis calculated at ωB97X-D/6-311 + G(d,p) level of theory.