College students’ social and eating jet lags and chronotypes may be related to irregular eating habits. Therefore, we examined the relationship between social and eating jet lags, chronotypes, variability in first and last mealtimes, and non-eating duration, as well as the effects of snacking between dinner and bedtime on social and eating jet lags, chronotypes, and mealtime variation. A total of 1900 Japanese male college students were recruited in this study. Mean wake-up time, bedtime, sleeping time, first and last mealtimes, snacks between meals, non-eating duration, the midpoint of non-eating duration, social and eating jet lags, and chronotype were calculated. Standard deviations in first and last mealtimes, the midpoint of non-eating duration, and the coefficient of variation in non-eating duration were used to evaluate mealtime variations. Mealtime variations were significantly associated with social and eating jet lags, chronotype, the midpoint of non-eating duration, and the difference in first and last mealtime between school holidays and class days. Chronotype and the midpoint of non-eating duration were significantly delayed with increased snacking after dinner. Mealtime variations were significantly lower in those who avoided snacking than in those who did not. Thus, social and eating jet lags and chronotypes are associated with sleep habits and mealtime irregularities.