Breakfast skipping and nighttime snacking have been identified as risk factors for obesity, diabetes, and cardiovascular diseases. However, the effects of irregularity of meal timing on health and daily quality of life are still unclear. In this study, a web-based self-administered questionnaire survey was conducted involving 4490 workers (73.3% males; average age = 47.4 ± 0.1 years) in Japan to investigate the association between meal habits, health, and social relationships. This study identified that irregular meal timing was correlated with higher neuroticism (one of the Big Five personality traits), lower physical activity levels, and higher productivity loss. Irregular meal timing was also associated with a higher incidence of sleep problems and lower subjective health conditions. Among health outcomes, a high correlation of irregular meal timing with mental health factors was observed. This study showed that irregularity of meal timing can be explained by unbalanced diets, frequent breakfast skipping, increased snacking frequency, and insufficient latency from the last meal to sleep onset. Finally, logistic regression analysis was conducted, and a significant contribution of meal timing irregularity to subjective mental health was found under adjustment for other confounding factors. These results suggest that irregular meal timing is a good marker of subjective mental health issues.