The structure determination of C16H20N6O4S, has shown that the molecule consists of two fused-ring systems joined by an S atom. Each ring system is nearly planar except for one sp(3) C atom. The mean S-C distance [1.730 (3) Angstrom] represents a bond order of 1.5. The bonding pattern of the pyrimidine-2,6-dione moiety is analysed in detail and compared with that of analogous compounds. The molecule is stabilized by intramolecular hydrogen bonds, while the intermolecular packing is governed by van der Waals forces.