The present work reports the development of a sensitive and selective method for ethinylestradiol detection using screen-printed electrode (SPE) modified with functionalized graphene (FG), graphene quantum dots (GQDs) and magnetic nanoparticles coated with molecularly imprinted polymers (mag@MIP). The performance of the mag@MIP sensor was compared with that of a non-molecularly imprinted sensor (mag@NIP). Chemical and physical characterizations of the mag@NIP and mag@MIP sensors were performed using scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS) and Brunauer-Emmett-Teller (BET) techniques. The electrochemical behavior of the electrodes investigated, which included (mag@MIP)-GQDs-FG-NF/SPE, (mag@NIP)-GQDs-FG-NF/SPE, GQDs-FG-NF/SPE and FG-NF/SPE, was evaluated by cyclic voltammetry. The results obtained show a significant increase in peak current magnitude for (mag@MIP)-GQDs-FG-NF/SPE. Using square wave voltammetry experiments, the efficiency of the (mag@MIP)-GQDs-FG-NF/SPE sensor was also tested under optimized conditions. The linear response range obtained for ethinylestradiol concentration was 10 nmol L−1 to 2.5 μmol L−1, with limit of detection of 2.6 nmol L−1. The analytical signal of the (mag@MIP)-GQDs-FG-NF/SPE sensor suffered no interference from different compounds and the sensor exhibited good repeatability. The proposed sensor was successfully applied for ethynilestradiol detection in river water, serum and urine samples, where recovery rates between 96 to 105% and 97–104% were obtained for environmental and biological samples, respectively.