Previous research has demonstrated that paradoxical sleep has a key role in learning and memory, and sleep deprivation interferes with learning and memory. However, the mechanism of memory impairment induced by sleep deprivation is poorly understood. The present study investigated the effect of paradoxical sleep deprivation (PSD) on spatial learning and memory using the Morris Water Maze. Effects of PSD on CA1 pyramidal neurons in hippocampus were also examined. PSD impaired spatial learning of rats. PSD induced translocation of Bax to mitochondria and cytochrome c release into the cytoplasm, and decreased the membrane excitability of CA1 pyramidal neurons, effects which may contribute to the deficits in learning behavior. These results may partially explain the mechanism of the effect of PSD on learning. Modulating the excitability of hippocampal neurons and protecting mitochondrial function are possible targets for preventing the effects of paradoxical sleep deprivation.