The electrochemical detection of methyl parathion in fish was performed by preconcentrating the pesticide on magnetic molecularly imprinted polymer and further readout on magneto-actuated electrode by square wave voltammetry. The magnetic molecularly imprinted polymer was synthesized by a magnetic core-shell strategy, using methacrylic acid as a functional monomer, and selected by theoretical calculation using the density functional theory (DFT). The characterization of this material was performed by SEM, TEM and XRD. Moreover, the binding capacity and selectivity towards methyl parathion was studied and compared with the corresponding magnetic non-imprinted polymer. The magneto-actuated electrochemical sensor showed outstanding analytical performance for the detection of methyl parathion in fish, with a limit of detection of as low as 1.22 × 10 −6 mg L −1 and recovery values ranging from 89.4% to 94.7%. The magnetic molecularly imprinted polymer successfully preconcentrated the analyte from the complex samples and paves the way to incorporate this material in other platforms for the detection of this pesticide in the field of environmental control and food safety.