In the title compound, C12H16N4S, the fused benzothiophene and the pyrimidine rings are coplanar [dihedral angle = 1.61 (6)°]. Three C atoms of the cyclohexene ring (at positions 3, 6 and 7) are disordered over two sites with an occupancy ratio of 0.702 (8):0.298 (8). The cyclohexene ring in both the major and minor components adopts a half-chair conformation. The crystal structure is stabilized by N—H⋯N and C—H⋯N interactions, resulting in the formation of inversion dimers with R
2
2(10) and R
2
2(12) graph-set motifs.