In this work, a novel method based on aptamers is proposed for electrochemical measurement of lysozyme. To this end, screen-printed carbon electrode (SPCE) was modified with a nanocomposite made from amino-reduced graphene oxide (Amino-rGO) synthesized from natural graphite powder, an ionic liquid (IL), and amino-mesosilica nanoparticles (Amino-MSNs). The composition of the nanocomposite (Amino-rGO/IL/Amino-MSNs) results in high thermal and chemical stability, conductivity, surface-to-volume ratio, cost efficiency, biocompatibility, and great bioelectrocatalysis characteristics. Presence of numerous amino groups, as well as remaining oxygen defects in rGO, provides a suitable site for immobilization of aptamers. Furthermore, use of this nanocomposite leads to considerable enhancement of the electrochemical signal and improved method sensitivity. Covalent coupling of aptamer’s amino groups with that of the nanocomposite using glutaraldehyde (GLA) as a linker helps immobilize amino-linked lysozyme aptamers (Anti-Lys aptamers) on nanocomposite. The modified electrode was characterized using electrochemical methods such as cyclic voltammetry (CV), differential pulse voltammetry (DPV), and electrochemical impedance spectroscopy (EIS). The immobilized aptamer selectively adsorbs lysozyme (Lys) on the electrode interface, leading to increased Charge Transfer Resistance (RCT) in EIS and decrease in the DPV peak currents which are used as analytical signals. Two separate calibration curves were drawn using the data acquired from EIS and DPV. The prepared anti-Lys aptasensor has two very low LODs equal to 2.1 and 4.2 fmol L−1 with wide detection ranges of 10 fmol L−1 to 200 nmol L−1, and 20 fmol L−1 to 50 nmol L−1 for EIS and DPV calibration curves, respectively. The SPCE/Amino-rGO/IL/Amino-MSNs/APT also showed high reproducibility, specificity, sensitivity, and rapid response to Lys which has various applications in fields of bioengineering and biomedicine.