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In the title complex, {[Co(C6H8N2O2)(C9H7NO2)(H2O)2](ClO4)2}n, the CoII ion lies on an inversion centre and is coordinated in a slightly distorted octahedral environment. The 2,5-dimethylpyrazine 1,4-dioxide ligand, which also lies on an inversion center, acts as a bridging ligand, linking symmetry-related CoII ions [Co...Co = 8.669 (3) Å] and forming one-dimensional chains along the b axis. In the crystal structure, these chains are linked by intermolecular aqua–perchlorate O—H...O hydrogen bonds, forming two-dimensional layers which are in turn connected into a three-dimensional network via π–π stacking interactions between quinoline rings, with a centroid–centroid distance of 3.580 (3) Å. An intermolecular O—H...Cl interaction is also present.