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In the title compound, C21H16FN3OS, the thieno[2,3-b]pyridine system forms dihedral angles of 10.57 (12) and 83.87 (5)° with the fluorophenyl ring at the 6-position and the phenyl ring of the benzyl group, respectively. In the crystal, molecules are linked by weak N—H...N anf N—H...O hydrogen bonds and π–π stacking interactions involving fluorophenyl rings of adjacent molecules, with a centroid–centroid distance of 3.648 (10) Å. In addition, intramolecular N—H...S and N—H...O hydrogen bonds contribute to the stability of the molecular conformation.