Recent evidence suggests that rapid eye movement (REM) sleep deprivation (REMSD) causes learning and memory deficits. However, the mechanism of REMSD-induced memory impairment remains unclear. Calcineurin (CaN) is involved in synaptic plasticity and is known as a negative constraint on learning and memory. Here we report that 72 h REMSD by the modified multiple platform method in rats resulted in spatial memory impairment in the Morris water maze and elevated hippocampal cytosolic CaN activity, both of which were reversed after 18 h sleep recovery. CaN expression in the whole-tissue homogenate of the hippocampus was not altered by REMSD. The results suggest that elevated hippocampal CaN activity is involved in REMSD-induced spatial memory impairment.