A magnetic particle assay has been designed herein that can report the interactions of DNA aptamers with their cognate protein targets lysozyme (LYS) and human thrombin (THR). Electrochemical sensing of the biomolecular recognition between each aptamer and its target was explored by using a disposable graphite electrode, PGE, in combination with differential pulse voltammetry (DPV). The magnitudes of the oxidation signals of LYS and THR were measured at +780 mV and +680 mV, respectively, after interaction with the cognate aptamers attached to the surface of magnetic particles. The detection limits estimated for signal to noise ratios above 3.0 correspond to the concentrations of 10.77 μg/mL LYS (769 nM) and 2.00 μg/mL THR (54.5 nM). Our aptamer based approach that combines magnetic particles with a disposable graphite electrode performs well compared to other aptamer-based sensor-formats for quantitative protein detection with respect to sensitivity, selectivity, detection limit, and reproducibility.