The determination of kanamycin sulfate was made indirectly by measuring its effect on photoluminescent amino functionalized graphene quantum dots (GQDs-amino) associated with gold nanoparticles (AuNPs) that were produced by the reduction of AuCl4 with NaBH4 in an aqueous dispersion of GQDs-amino (obtained by the pyrolysis of citric acid and glutathione) also containing the cationic surfactant CTAB. The AuNPs-GQDs-amino-CTAB system presents a suppressed photoluminescence that is amplified in the presence of kanamycin. Under optimized experimental conditions, the photoluminescence amplification of the nanomaterial system showed a linear response as a function of kanamycin concentration, covering three orders of magnitude (10−7 to 10−5molL−1). The use of solid phase extraction with a cartridge packed with aminoglycoside selective molecularly imprinted polymer ensured selectivity in determinations made on yellow-fever vaccine and veterinary pharmaceutical formulations. The analytical results were statistically similar to those obtained with an HPLC-based fluorescence method (after chemical derivatization). The proposed method is a simple, sensitive and selective approach that does not involve the use of toxic reagents employed for chemical derivatization of aminoglycoside antibiotics.