Background Some people can subconsciously wake up naturally (self-awakening) at a desired/planned time without external time stimuli. However, the underlying mechanism regulating this ability remains to be elucidated. This study sought to examine the relationship between hemodynamic changes in oxyhemoglobin (oxy-Hb) level in the prefrontal cortex and sleep structures during sleep in subjects instructed to self-awaken. Results Fifteen healthy right-handed male volunteers with regular sleep habits participated in a consecutive two-night crossover study. The subjects were instructed to wake up at a specified time (“request” condition) or instructed to sleep until the morning but forced to wake up at 03:00 without prior notice (“surprise” condition). Those who awoke within ± 30 min of the planned waking time were defined as those who succeeded in self-awakening (“success” group). Seven subjects succeeded in self-awakening and eight failed. No significant differences were observed in the amounts of sleep in each stage between conditions or between groups. On the “request” night, an increase in oxy-Hb level in the right prefrontal cortex and a decrease in δ power were observed in the “success” group around 30 min before self-awakening, whereas no such changes were observed in the “failure” group. On the “surprise” night, no significant changes were observed in oxy-Hb level or δ power in either group. Conclusions These findings demonstrate a correlation between self-awakening and a pre-awakening increase in hemodynamic activation in the right prefrontal cortex, suggesting the structure’s contribution to time estimation ability.