Enrofloxacin (ENR), as one of the fluoroquinolone antibiotics with broad applications, is stable, can lead to bacterial resistance, environmental challenges and health issues. Thus, selective detection and separation methods for ENR are required in the monitoring of residues in food and environmental mediums. The objective of this work was to synthesize and characterize a core-shell magnetic molecularly imprinted polymer (MIP) electrochemical sensor for selective detection and separation of ENR. In this study, ENR was characterized using Ultraviolet–visible (UV-Vis) and high-performance liquid chromatography (HPLC). Superparamagnetic iron-oxide nanoparticles (SPIONs) were synthesized, coated and grafted with silica and MIP, respectively. Other characterization process was conducted via dynamic light scattering (DLS), transmission electron microscopy (TEM), vibrating sample magnetometer (VSM), and electrochemical studies. The MIP performance was evaluated by assessment of binding capacity, selectivity, and electrochemical detection via screen-printed carbon electrodes (SPCEs). Results confirmed efficient synthesis of core-shell nanomagnets (60-120 nm) with very good magnetic response (40 emu/g). MIP had good ENR binding capacity (imprinting factor=8.92) and specificity but with weak cross-reactive response to ciprofloxacin and norfloxacin. Electrochemical detection was linear in the range 10-400 µg/mL (LOD=2.1 µg/mL, R2=0.9945) with very good stability (96% relative signal retained after 30 days). The repeatability (RSD=3.4%) and magnetic separability of the sensor make it useful for real-world applications. This work implies new integration of magnetic separation methodologies and molecularly imprinted technology towards the aim to reach sensitive and selective detection of ENR.