We introduce an innovative electrochemical sensing method for the sensitive detection of Baicalein (BAI), emphasizing a simple surface modification process. The study encompasses both practical and theoretical investigations into the electrochemical behavior of nanoporous gold. Our theoretical analysis, based on advanced quantum-mechanical calculations, demonstrates that the adsorption of BAI molecule on gold-based substrates is energetically favorable, with adsorption energy increasing from an unmodified surface to a more porous substrate. BAI physisorbs on unmodified regions in a horizontal alignment, while it chemisorbs more strongly on nanoporous regions by penetrating the pores. On less modified surfaces, interaction energy predominates, whereas on heavily modified surfaces, distortion energies become more significant due to increased substrate reactivity. These results align with physicochemical characterizations, which reveal that nanoscale modifications, induced by different anodization times, explain the variations in electrode performance. Experimentally, cyclic voltammetry (CV) and differential pulse voltammetry (DPV) were employed using both a gold electrode (GE) and a nanoporous gold electrode (NPGE). The GE was subjected to surface treatment by immersion in H2SO4 and potential control at ca. +2.0 V for 40 seconds, resulting in a nanoporous configuration. Following optimizations, Adsorptive Stripping Voltammetry (AdSV) was used to determine BAI. The method achieved detection (LOD) and quantification (LOQ) limits of 0.015 µmol L-1 and 0.045 µmol L-1, respectively (Edeposition=-0.25 V; tdeposition=50 s). Additionally, the standard addition method was applied to the NPGE for recovering BAI from spiked synthetic human plasma and urine, with success rates ranging from 93.4% to 106%. This approach exhibited excellent stability, precision, and accuracy, with minimal interference from other substances. Moreover, the theoretical findings provided deeper insights into the selective electrochemical detection of BAI on nanoporous gold surfaces, offering new perspectives on this field.