Herein, we propose a highly sensitive and selective three-dimensional electrochemical paper-based analytical device (3D-ePAD) to determine serotonin (Ser). It uses a graphite-paste electrode modified with nanoparticles coated with molecularly imprinted polymer (MIP). FeO@Au nanoparticles were encapsulated with silica to create novel nano-sized MIP. Morphology and structural characterization reveal that silica imprinted sites (FeO@Au@SiO) synthesized via sol-gel methods provide excellent features for Ser detection, including high porosity, and greatly improve analyte diffusion and adsorption to provide a faster response by the MIP sensor. The template molecule was effectively removed by solvent extraction to provide a greater number of specific cavities that enhance analyte capacity and sensitivity. The 3D-ePAD was fabricated by alkyl ketene dimer (AKD)-inkjet printing of a circular hydrophobic detection zone on filter paper for application of aqueous samples, coupled with screen-printed electrodes on the paper, which was folded underneath the hydrophobic zone. The sensor was constructed by drop coating of FeO@Au@SiO-MIP nanocomposites on the graphite electrode (GPE) surface. The MIP sensor (FeO@Au@SiO-MIP/GPE) was used in the detection of Ser by linear-sweep voltammetry (LSV) in 0.1 M phosphate buffer at pH 8.0. The device exhibits high sensitivity toward Ser, which we attribute to synergistic effects between catalytic properties, electrical conductivity of FeO@Au@SiO, and significantly increased numbers of imprinted sites. Ser oxidation was observed at +0.39 V. Anodic peak currents for Ser show linearity from 0.01 to 1000 μM (y = 0.0075 ± 0.0049 x + 0.4071 ± 0.0052, r = 0.993), with a detection limit of 0.002 μM (3S/N). The device provides good repeatability (%relative standard deviations; RSD) = 4.23%, calculated from the current responses of ten different MIP sensors). The device also exhibits high selectivity and reproducibility (%RSD = 8.35%, obtained from five calibration plots). The analytical performance of the device is suitable for the determination of Ser in pharmaceutical capsules and urine samples.