Abstract Introduction Sleep deprivation can impair time perception. In a sleep-deprived state, time tends to be overestimated. In addition, sleep deprivation can affect circadian fluctuations in time perception. Time perception may also fluctuate at rhythms other than circadian rhythms, such as theta frequency. Previous studies have shown that perceived time can fluctuate at theta frequencies and that such fluctuations are a function of the cue-to-target interval for the response. However, whether sleep deprivation affects theta fluctuations in time perception is unknown. Methods In this study, we compared a sleep deprivation condition with a normal sleep condition that served as an experimental control. In both conditions, participants (N=24, 13 females, mean age 25.6±3.5 years) were asked to complete a task to generate 3 seconds of time by pressing a key before and after sleep or sleep deprivation time (23:00 to 8:00). The interval between the clue (cueing that a response signal will appear) and the response signal (requiring 3 seconds to be generated as soon as possible) was designed to range from 0.25 to 1.05 seconds in steps of 1/30th of a second. Results As a result, similar to previous studies, an overestimation of time was observed in the case of sleep deprivation. In addition, stronger fluctuations in time perception were found at low theta frequencies (4.4 to 4.8 Hz) in the case of sleep deprivation. Conclusion This study suggests that cognitive abilities such as time perception fluctuate at different rhythms, and sleep deprivation may affect these fluctuations. These fluctuations may be associated with instability of brain states and functions (e.g., attention) due to sleep deprivation. Further studies are needed to elucidate the neurophysiological mechanisms. Support (if any) JSPS Foreign Researcher Scholarship, JSPS KAKENHI (Grants No. JP17K19639), AMED (Grants No. JP21zf0127005), and World Premier International Research Center Initiative (WPI), MEXT, Japan.