This study investigates the structural basis for urate recognition and the inhibitory effect of apigenin on human GLUT9, a high-capacity urate transporter. Cryo-electron microscopy (cryo-EM) structures of human GLUT9 in complex with urate or apigenin at resolutions of 3.5 Å and 3.3 Å, respectively, reveal that GLUT9 exhibits an inward-open conformation with the substrate binding pocket facing the intracellular side. These structures explain why urate is preferentially transported by GLUT9 over glucose and show that apigenin acts as a competitive inhibitor by occupying the substrate binding site. The findings provide critical insights for the development of specific inhibitors targeting GLUT9 as potential therapeutics for gout and hyperuricemia. The study also highlights the importance of specific residues in urate recognition and the stability of the GLUT9-urate complex compared to the glucose complex, offering a rationale for the substrate preference of urate over glucose. Additionally, the binding poses of apigenin and the residues involved in its binding are identified, providing a basis for drug optimization.This study investigates the structural basis for urate recognition and the inhibitory effect of apigenin on human GLUT9, a high-capacity urate transporter. Cryo-electron microscopy (cryo-EM) structures of human GLUT9 in complex with urate or apigenin at resolutions of 3.5 Å and 3.3 Å, respectively, reveal that GLUT9 exhibits an inward-open conformation with the substrate binding pocket facing the intracellular side. These structures explain why urate is preferentially transported by GLUT9 over glucose and show that apigenin acts as a competitive inhibitor by occupying the substrate binding site. The findings provide critical insights for the development of specific inhibitors targeting GLUT9 as potential therapeutics for gout and hyperuricemia. The study also highlights the importance of specific residues in urate recognition and the stability of the GLUT9-urate complex compared to the glucose complex, offering a rationale for the substrate preference of urate over glucose. Additionally, the binding poses of apigenin and the residues involved in its binding are identified, providing a basis for drug optimization.