In the title compound, C5H8N3O+·ClO4
−·C5H7N3O·H2O, each perchlorate anion is paired with a protonated cationic 2-amino-6-methylpyrimidin-4(1H)-one and another non-protonated entity of the same organic pyrimidinone. The crystal structure is stabilized by N—H⋯Oorg, N—H⋯Owater, N—H⋯OClO4, O—H⋯OClO4, N—H⋯N and C—H⋯OClO4 hydrogen bonds between the anions, organic entities and water molecules. Intermolecular π–π stacking interactions between neighbouring organic rings are observed with a face-to-face distance of 3.776 (2) Å, and O—H⋯O hydrogen bonds link the perchlorate anions and the water molecules into chains along the b-axis direction. The perchlorate anion and the interstitial water molecule are disordered over two mutually incompatible positions with a common occupancy ratio of 0.678 (16):0.322 (16).