The assessment of fish welfare is crucial to prevent economic losses in aquaculture and ensure reliable results in research. A quick, non-invasive device to measure cortisol levels in fish farm water facilitates welfare evaluation and corrective actions when compromised. To address this need, an innovative sensor was developed using screen-printed carbon electrodes (SPCEs) functionalized with reduced graphene oxide/Prussian blue nanocubes (rGO/PBNCs) for direct selective detection of cortisol. A molecularly imprinted polymer (MIP) was synthesized on rGO/PBNCs/SPCEs by electropolymerization (ELP) of pyrrole in the presence of cortisol. The polymerization solution was prepared by adding cortisol (5 mM) and pyrrole (0.3 M) to a DMF/PBS (1:4) solution (pH 7.4). Following ELP, the electrodes were washed with PBS, and pyrrole overoxidation was used to extract cortisol from the polymer matrix. For comparison purposes, a non-imprinted polymer (NIP) was also fabricated. The electrodes were characterized using scanning electron microscopy (SEM) and Raman spectroscopy to assess their morphological and chemical features. Under optimized conditions, the sensor showed a linear range from 0.1 nM to 0.1 mM in artificial saltwater. This sensor combines simplicity and affordability while providing reliable detection of chemical and biological compounds.