Study Objectives: Sleep-wake regularity (SWR) is often disrupted in college students and mood disorders are rife at this age. Disrupted SWR can cause repetitive and long-term misalignment between environmental and behavioral cycles and the circadian system which may then have psychological and physical health consequences. We tested whether SWR was independently associated with mood and autonomic function in a healthy adult cohort. Methods: We studied 42 college students over a 3 week period using daily sleep-wake diaries and continuous electrocardiogram recordings. Weekly SWR was quantified by the interdaily stability of sleep-wake times (ISSW) and mood was assessed weekly using the Beck Depression Inventory-II. To assess autonomic function, we quantified the high-frequency (HF) power of heart rate variability (HRV). Linear mixed effects models were used to assess the relationship between repeated weekly measures of mood, SWR, and HF. Results: Low weekly ISSW predicted subsequent poor mood and worsening mood independently of age, sex, race, sleep duration, and physical activity. Although no association was found between ISSW and HF, the ISSW-mood association was significantly moderated by nocturnal HF, i.e. reported mood was lowest after a week with low ISSW and high HF. Prior week mood scores did not significantly predict the subsequent week's ISSW. Conclusions: Irregular sleep-wake timing appears to precede poor mood in young adults. Further work is needed to understand the implications of high nocturnal HRV in those with low mood and irregular sleep-wake cycles.