The development of a reliable electrochemical sensor using a hybrid nanocomposite consisting of ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate) functionalized graphene oxide (GrO-IL) and gold nanoparticles (AuNPs) stabilized by chitosan (Chit) was described. The new sensor, labelled as GrO-IL-AuNPs-Chit/CSE, exhibited an improved electrocatalytic response to cancer drugs such as purine antimetabolites (6-thioguanine, 6-mercaptopurine, and azathioprine) in a wide concentration range with a low detection limit (20-40 nmol·L-1, S/N = 3), and satisfactory recoveries (97.1-103.0%). The sensor has been also successfully used for cyclic voltammetric study of a salmon sperm double-stranded DNA degradation and DNA-6-mercaptopurine interaction in aqueous solutions (pH 7.4).