A novel polymeric nanosensor (named PEINAC) based on polyethyleneimine (PEI), was designed for the selective fluorescence detection of l-lysine (L-Lys) in aqueous solutions. The sensor was synthesized through a one-step, three-component reaction involving orthophthalaldehyde (OPA), PEI, and acetylcysteine. This reaction simultaneously facilitated the creation of an isoindole fluorophore, which was chemically attached to the PEI backbone. The structural properties, size, and morphology of PEINAC were thoroughly analyzed using various characterization techniques. When introduced into a buffered solution at pH 7.0, PEINAC demonstrated high specificity for L-Lys, inducing a marked fluorescence enhancement at 450 nm upon excitation at 367 nm. The fluorescence intensity exhibited a linear relationship with L-Lys concentration, ranging from 1 μM to 1000 μM, with a detection limit of 0.13 μM. Notably, the sensor exhibited excellent selectivity, showing no significant interference from other biomolecules and common transition metal ions and anions. This sensor was successfully applied for L-Lys quantification in blood and urine samples and for cellular L-Lys imaging, demonstrating its potential in various analytical and biomedical applications.