The N-methyl-d-aspartate receptor antagonist, MK-801, is widely used to induce memory and learning impairments in preclinical studies. MK-801 is mainly injected intraperitoneally (i.p.) at doses that result in cognitive impairment and induction of motor or sensory disturbances. The aim of this study was to compare the behavioral outcomes when different administration routes (subcutaneous (s.c.) and i.p.) and MK-801 doses (0.01, 0.05, and 0.1 mg/kg) are employed in the Morris water maze (MWM) task. We also assessed the pharmacokinetics of MK-801 in rat blood plasma and its bioavailability in brain tissue. The concentrations of MK-801 in brain tissue and blood plasma were significantly higher after s.c. than i.p. administration. MK-801 administered via the s.c. route at doses of 0.1 and 0.05 mg/kg significantly impaired learning on all training days in the MWM task compared to i.p. administration at the same doses. Memory in the probe trial was significantly impaired after MK-801 administration via both routes at all doses. MK-801 also induced locomotor disturbances after i.p. and s.c. administration at the highest dose (0.1 mg/kg). Our data suggest that s.c. administration leads to higher MK-801 concentrations in brain tissue and blood plasma and evidently impairs spatial learning and memory compared to i.p. administration at the same dose. Knowledge of MK-801 concentrations in the brain and blood and the effects of the compound on memory processes and locomotor activity enable the choice of more targeted routes and doses of administration in preclinical studies.