Hypobaric hypoxia (HH), a predisposing environmental condition at high altitude (HA) encountered by many mountaineers jeopardizes their normal physiology like motor coordination and cognitive functions. Our previous studies revealed that the HH induces oxidative stress and neurodegeneration, which is associated with spatial memory impairment in rats. However, the dendritic changes after exposure to different duration of HH remain largely unknown. The aim of the present study was to investigate the duration-dependent dendritic changes in CA1, CA3 and entorhinal cortex (EC) of hippocampus and layer II of prefrontal cortex (PFC) with spatial memory functions in rats on exposure to different duration of HH. The rats were exposed to simulated HA of 6100 m for 3, 7, 14 and 21 days and the spatial reference memory was investigated using Morris water maze (MWM) and the morphological alteration of CA1, CA3, EC and layer II of PFC were investigated. There was a significant decrease in dendritic arborization and spine number along with increased number of damaged neurons, after 3, 7 and 14 days of HH but after 21 days of HH exposure the structural recovery was noted in all the regions. There was impairment of spatial memory after 3 and 7 days of exposure, but slight improvement of spatial memory was noted after 14 and 21 days of exposure. Our studies suggested that HH induces dendritic plasticity of PFC and hippocampal pyramidal neurons of rat brain, which might be associated with improvement of spatial memory function after 21 days of HH exposure.