The electrochemical oxidation of an antiviral drug, ganciclovir (GCV) at Fe3O4/carboxylated multi-walled carbon nanotubes modified glassy carbon electrode (Fe3O4/cMWCNTs/GCE) was studied by voltammetric techniques. The influence of the effective parameters on the electrochemical behavior of GCV was investigated. Under optimized conditions, the proposed sensor was applied for low level GCV determination. The relationship between peak current and the concentration of GCV was linear in the range of 80–53,000nM with a detection limit of 20nM through square wave voltammetry (SWV). The interaction of GCV with calf thymus DNA was also explored by voltammetric and spectrofluorometric methods. Based on the obtained data the mode of binding of GCV to DNA was intercalative binding. The decrease in the SWV peak current of GCV in the presence of DNA was used for the determination of DNA. The modified electrode exhibited a good sensitivity, stability and pleasant reproducibility, and it was applied for the determination of GCV in spiked serum and urine, with satisfactory results.