Lunar habitation and exploration of space beyond low-Earth orbit will require small crews to live in isolation and confinement while maintaining a high level of performance with limited support from mission control. Astronauts only achieve approximately 6 h of sleep per night, but few studies have linked sleep deficiency in space to performance impairment. We studied crewmembers over 45 days during a simulated space mission that included 5 h of sleep opportunity on weekdays and 8 h of sleep on weekends to characterize changes in performance on the psychomotor vigilance task (PVT) and subjective fatigue ratings. We further evaluated how well bio-mathematical models designed to predict performance changes due to sleep loss compared to objective performance. We studied 20 individuals during five missions and found that objective performance, but not subjective fatigue, declined from the beginning to the end of the mission. We found that bio-mathematical models were able to predict average changes across the mission but were less sensitive at predicting individual-level performance. Our findings suggest that sleep should be prioritized in lunar crews to minimize the potential for performance errors. Bio-mathematical models may be useful for aiding crews in schedule design but not for individual-level fitness-for-duty decisions.