In the title compound, C(16)H(12)F(4)N(2)O(3)S, the pyrimidine ring adopts a half-chair conformation; the mean plane formed by the ring atoms excluding the C atom bonded to the thio-phen-2-ylcarbonyl group has an r.m.s. deviation of 0.059 Å. The dihedral angle between the benzene and thio-phene rings is 62.26 (7)°. The mol-ecular conformation is stabilized by an intra-molecular O-H⋯O hydrogen bond, generating an S(6) ring. In the crystal, adjacent mol-ecules are connected via a centrosymmetric R(2) (2)(6) motif, formed by N-H⋯O hydrogen bonds.