Lysozyme (LYS) applications encompass anti-bacterial activity, analgesic, and anti-inflammatory effects. In this work, a porous framework that was based on the polymerization of pyrrole (PPy) in the presence of multi-functional graphene oxide/iron oxide composite (GO@Fe3O4) has been developed. Oxygen-containing and amine groups that were present in the nanocomposite were availed to assembly LYS as the molecularly imprinted polymer (MIP) template. The synthesized material (MIPPy/GO@Fe3O4) was electrodeposited on top of a gold microelectrode array. Transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS) were used to confirm the adequate preparation of GO@Fe3O4, and the characterization of the resulting molecularly imprinted electrochemical sensor (MIECS) was carried out by electrochemical impedance spectrometry (EIS), FT-IR analysis, and scanning electron microscopy (SEM). The impedimetric responses were analyzed mathematically by fitting to a Q(Q(RW)) equivalent circuit and quantitative determination of LYS was obtained in a linear range from 1 pg/mL to 0.1 µg/mL, presenting good precision (RSD ≈ 10%, n = 5) and low limit of detection (LOD = 0.009 pg/mL). The fabrication of this device is relatively simple, scalable, rapid, and economical, and the sensor can be used up to nine times without disintegration. The MIECS was successfully applied to the determination of LYS in fresh chicken egg white sample and in a commercial drug, resulting in a straightforward platform for the routine monitoring of LYS.