The synthesis and structure of a lead(II) complex of the flavonoid morin is hereby reported. This is the first example of a Pb(II) complex depicting an active inert pair effect with a flavonoid (morin). The complex has an orthorhombic structure with space group P212121. The complex shows a distorted square-based pyramidal coordination geometry. The average metal ion to donor atom coordination bond length (Pb−O) is 2.553 Å for five O-donors from water, perchlorate ions, and the morin ligand. The metal is coordinated to the morin's carbonyl and the hydroxyl oxygen at position 3. The coordination sphere of the core metal ion at the site of the lone pair on Pb(II) is devoid of any donor atom. The crystal packing features an offset face-to-face intermolecular π–π interaction with morin's centroid–centroid distances averaging 3.4 Å and displacement angles of 11.81o. Theoretical calculations using density functional theory (DFT) supported the empirical results. The DFT calculations showed that the presence of an active inert electron pair in the morin-Pb(II) complex lowers its ground state energy.