Study objective: To elucidate the contribution of time estimation and pre sleep arousal to the component of sleep onset misperception not explained by sleep fragmentation. Methods: At-home ambulatory polysomnograms (PSGs) of 31 people with insomnia were recorded. Participants performed a time estimation task and completed the Pre Sleep Arousal Scale (PSAS). Based on previous modelling of the relationship between objectively measured sleep fragmentation and sleep onset misperception, the subjective sleep onset was estimated for each participant as the start of the first uninterrupted sleep bout longer than 30 min. Subsequently, the component of misperception not explained by sleep fragmentation was calculated as the residual error between estimated sleep onset and perceived sleep onset. This residual error was correlated with individual time estimation task results and PSAS scores. Results: A negative correlation between time estimation task results and the residual error of the sleep onset model was found, indicating that participants who overestimated a time interval during the day also overestimated their sleep onset latency (SOL). No correlation was found between PSAS scores and residual error. Conclusions: Interindividual variations of sleep architecture possibly obscure the correlation of sleep onset misperception with time estimation and pre sleep arousal, especially in small groups. Therefore, we used a previously proposed model to account for the influence of sleep fragmentation. Results indicate that time estimation is associated with sleep onset misperception. Since sleep onset misperception appears to be a general characteristic of insomnia, understanding the underlying mechanisms is probably important for understanding and treating insomnia.