Quantified-self sleep tracking devices such as Fitbit are gaining great popular in recent years. However, users often complain about the discrepancy between the data collected with sleep trackers and their subjective sleep experience, which is often attributed to the accuracy issue of the devices. In this pilot study, we aim to provide an explanation to such discrepancy from a neuroscience perspective. We investigated the associations of subjective sleep rating and Fitbit measured sleep data to cortical hemodynamics in the prefrontal cortex (PFC) during the first sleep cycle. Correlation analysis results showed that subjective sleep rating mainly correlated to the median of the concentration changes in oxyhemoglobin (ΔO2Hb) and deoxyhemoglobin (ΔHHb) in a set of channels, with positive correlation coefficients. In contrast, the sleep score computed by Fitbit mainly correlated to the mean of the ΔO2Hb and ΔHHb in a different set of channels, with negative correlation coefficients. The findings suggested that better perceived sleep quality may be positively associated to increased hemodynamics during the first sleep cycle, and the opposite may be true for objective sleep metrics such as sleep score measured by Fitbit. The result implies that users’ subjective perception of sleep and the sleep tracking devices may be capturing different dimensions of sleep. As such, improving device accuracy may help little in addressing the discrepancy between the subjective sleep experience and the objective data. The findings provided design implications for the development of future sleep tracking technologies.