Due to the high importance of Staphylococcus aureus alpha-toxin in poisoning and pathogenicity of this bacterium, we developed a sensitive and selective sensor based on gold nanoparticle/multi-walled carbon nanotubes modified carbon paste electrode and 1-butyl-3-methylimidazolium hexafluorophosphate as a binder for electrochemical detection of alpha-toxin. The prepared nanocomposite was characterized by transmission electron microscopy, scanning electron microscopy, dynamic light scattering, energy dispersive X-ray analysis, and UV-visible spectra. The square wave voltammetry as a sensitive technique was selected for the quantification of alpha-toxin. Electrochemical behavior of unmodified and modified electrode, the type and pH value of supporting electrolyte, and scan rate were done for quantification of alpha-toxin. To determine the specificity of the aptasensor, the interference of some serum markers were also examined. The linear range and detection limit were calculated at 3.0-250.0 nM and 1.0 nM, respectively. The relative standard deviations for 5.0 nM and 100.0 nM alpha-toxin were obtained 1.15-0.83%, respectively. None of the interfering factors were involved in measuring the concentration of 120.0 nM alpha-toxin. Therefore, the introduced aptasensor with high sensitivity, selectivity, and repeatability, was used for the determination of alpha-toxin in the serum sample.