This study presents the design and application of an electrochemical sensor for selective detection of lead ions (Pb²⁺) based on ionophore-modified raspberry-like Fe₃O₄–Au nanostructures. The material was engineered with a magnetic Fe₃O₄ core, coated with polyethyleneimine (PEI) to facilitate nucleation, and subsequently decorated with Au nanoparticles, providing a raspberry-like (Fe₃O₄@PEI@AuNPs) nanostructure with high surface area and excellent electrochemical conductivity. Surface functionalization with Lead Ionophore IV (ionophore thiol) introduced Pb²⁺-selective binding sites, whose presence and structural evolution were verified by TEM and Raman spectroscopy. The Fe₃O₄ core endowed strong magnetic properties, enabling facile manipulation and immobilization onto screen-printed carbon electrodes (SPCEs) via physical adsorption, while the Au nanoparticles enhanced electron transfer, supplied thiol-binding sites for stable ionophore anchoring, and increased the effective electroactive surface area. Operational conditions were systematically optimized, with acetate buffer (HAc/NaAc, pH 5.7) and chronoamperometric preconcentration (CA) at −1.0 V for 175 s identified as optimal for differential pulse voltammetry (DPV) measurements. Under these conditions, the sensor exhibited a linear response toward Pb²⁺ from 0.025 mM to 2.00 mM with superior sensitivity and reproducibility compared to conventional AuNP-modified SPCEs. Furthermore, the ionophore-modified Fe₃O₄–Au nanostructure-based sensor demonstrated outstanding selectivity for Pb²⁺ over competing heavy metal ions (Cd²⁺, Hg²⁺, Cr³⁺), owing to the specific coordination interaction of Lead Ionophore IV with target ions. These findings highlight the potential of raspberry-like Fe₃O₄@PEI@AuNP nanostructures as a robust and efficient electrochemical platform for the sensitive and selective detection of toxic heavy metal ions.