Value of the data 1.The data present concentrations of MK-801 in mouse brain tissue and plasma after s.c. and i.p. administration, which is important for experiment planning in experimental neuroscience. 2.These data will help researchers to choose the right administration route of MK-801 in the animal experiments. 3.The developed MK-801 quantification method (SPE and UPLC-MS/MS) can be used to determine MK-801 in mammalian tissue samples. 4.The data presented in this data article show that the concentration of MK-801 in brain tissues and plasma depend on the route of administration.