An electroanalytical method using square wave voltammetry (SWV) is proposed for the quantification of Guanine (G), 6‐Thioguanine (TG), Acyclovir (Acy) and Ganciclovir (Gan) in different types of pharmacological samples. In addition, for the first time, a study of the electrochemical behavior (using cyclic voltammetry, CV) of guanine and its pharmacological derivatives on fluoride doped oxide (FTO) electrodes was carried out. The study of CV potential scanning demonstrated the charge transfer process was diffusion controlled and the diffusion coefficient was determined for all the studied products. Besides, electrochemical parameters, such as transfer coefficient, heterogeneous charge transfer constant and the number of electrons transferred (e) were determined namely, 4e for TG and 2e for G, Acy and Gan. SWV studies at pH 4 for G and 2 for TG, Acy and Gan showed linear ranges between 4.0×10−6 and 40.0×10−6 mol L−1, with detection limits of 0.91×10−6 for G, and 1.50×10−6 for TG, 1.25×10−6 for Acy and 0.45×10−6 mol L−1 for Gan. The method presents sensitivity and stability appropriate to be employed in quality control and routine quantification of drugs in pharmaceutical formulations.