In the title compound, C(15)H(12)F(3)N(3)O(3)S, the pyrimidine ring adopts a half-chair conformation with the mean plane formed by the ring atoms excluding the C atom bonded to thio-phene-2-carbonyl group lying nearly perpendicular to the pyridine and thio-phene rings, making dihedral angles of 84.91 (4) and 87.40 (5)°, respectively. The dihedral angle between the pyridine and thio-phene rings is 54.44 (5)°. The crystal structure is stabilized by inter-molecular O-H⋯O and N-H⋯N hydrogen bonds and weak C-H⋯O inter-actions further consolidate the structure.