A novel potentiometric microelectrode incorporating a molecularly imprinted polymer (MIP) was fabricated, characterized, and successfully applied to the recognition and quantification of the drug, metronidazole benzoate. The elaborated MIP-based sensor was realized by thermal polarization, using metronidazole benzoate as the template material, 1-vinyl-2-pyrrolidine (VP) as a functional monomer, and ethylene glycol dimethacrylate (EGDMA) as the cross-linking agent in the presence of benzoyl peroxide as the initiator. The MIP-based sensor exhibited a super-Nernstian response (61.5 ± 0.5, mV/decade) covering the linear concentration range of 1 × 10−8–1 × 10−3 mole L−1 of metronidazole benzoate with a fast response time (≤10, s.) and detection limit of 7 × 10−9 mole L−1. The microchip showed high selectivity toward the template drug molecule in the presence of many investigated interfering species. The chip electrode was successfully used in the quantification of metronidazole benzoate in some real biological samples with high accuracy (recovery, 95.4%) and precision (RSD, 1.5). Moreover, the merits offered by the elaborated MIP-based MB microchip assembly include small size, miniaturization, integration, and consequently, automation feasibility.