Rapid-eye movement sleep deprivation (REM SD) drastically alters behavioral functions and the mood state. Evidence demonstrates that the effects of REM SD on cognition and mood vary significantly based on the duration of deprivation. On the other hand, crocin (as a natural therapeutic compound found in Saffron) may be beneficial for the alleviation of SD effect. The present research aimed to explore the effects of REM SD of varying durations on behavioral functions and the expression levels of brain-derived neurotrophic factor (BDNF) and glycogen synthase kinase-3 beta (GSK-3β) in the prefrontal cortex. REM SD was conducted for 1, 5, or 10 days (6 h per day). Crocin was injected intraperitoneally at the dose of 50 mg/kg. The results showed that REM SD for 5- and 10-days increased locomotor activity and rearing, decreased pain threshold, and impaired passive avoidance memory performance. REM SD for 5- and 10-days increased the expression levels of GSK-3β, while only REM SD for 5 days decreased BDNF levels. Crocin (only in rats exposed to REM SD for 5 days) restored behavioral alterations, while in rats exposed to REM SD for 10 days had no effect. Interestingly, crocin in rats exposed to REM SD for 5- and 10-days attenuated GSK-3β upregulation. In addition, crocin in rats exposed to REM SD for 5 but not 10 days attenuated BDNF down regulation. In conclusion, the duration of REM SD is a crucial determinant of its impact on cognitive and mood functions.