Social jetlag (SJ) occurs when sleep-timing irregularities from social or occupational demands conflict with endogenous sleep–wake rhythms. SJ is associated with evening chronotype and poor mental health, but mechanisms supporting this link remain unknown. Impaired ability to retrieve extinction memory is an emotion regulatory deficit observed in some psychiatric illnesses. Thus, SJ-dependent extinction memory deficits may provide a mechanism for poor mental health. To test this, healthy male college students completed 7–9 nights of actigraphy, sleep questionnaires, and a fear conditioning and extinction protocol. As expected, greater SJ, but not total sleep time discrepancy, was associated with poorer extinction memory. Unexpectedly, greater SJ was associated with a tendency toward morning rather than evening chronotype. These findings suggest that deficient extinction memory represents a potential mechanism linking SJ to psychopathology and that SJ is particularly problematic for college students with a greater tendency toward a morning chronotype.