In the title salt, C 6H 10N 3O 2 +·C 5H 3O 2S −, the 2-amino-4,6-dimethoxypyrimidinium cation interacts with the carboxylate group of the thiophene-2-carboxylate anion through a pair of N—H⋯O hydrogen bonds, forming an R 2 2(8) ring motif. These motifs are centrosymmetrically paired via N—H⋯O hydrogen bonds, forming a complementary DDAA array. The separate DDAA arrays are linked by π–π stacking interactions between the pyrimidine rings, as well as by a number of weak C—H⋯O and N—H⋯O interactions. In the anion, the dihedral angle between the ring plane and the CO 2 group is 11.60 (3)°. In the cation, the C atoms of methoxy groups deviate from the ring plane by 0.433 (10) Å.