In this study, a novel and simple magnetic electrochemical sensing protocol for the sensitive detection of Hg(II) in aqueous media was demonstrated. For this purpose, the halloysite nanotubes-iron oxide–manganese oxide nanocomposite (HNTs-Fe3O4–MnO2) was successfully synthesized for the first time. The synthesis process involves the deposition of Fe3O4 nanoparticles on the surface of HNTs using a simple chemical precipitation method, subsequent formation of wire-like MnO2 nanoparticles on the surface of HNTs-Fe3O4 composites by hydrothermal method with potassium permanganate (KMnO4) and ammonium persulfate ((NH4)2S2O8). The resulting HNTs-Fe3O4–MnO2 nanocomposite was suspended in mercury solution and then brought on the surface of a magnetic carbon paste electrode (MCPE). The amount of analyte was detected electrochemically by applying differential pulse voltammetry (DPV). The conditions of extraction and voltammetric determination were studied and optimized. The proposed method exhibited a linear relationship towards Hg(II) concentrations ranging from 0.5 to 150μgL−1. The detection limit achieved was 0.2μgL−1 (3Sb/m), which is lower than the US Environmental Protection Agency (EPA) standard (2μgL−1 for drinkable water). The proposed methodology was applied for quantification of Hg(II) in real water samples and good recoveries were obtained from 96.0 to 102.7%.