Breakfast skipping (BS) has been considered to be associated with obesity, particularly among younger generations. However, few studies have addressed this issue in a middle-aged population considering sex and the conditions prior to breakfast. Therefore, we investigated clinical parameters, self-reported BS, late-night dinner (LND) eating, and late-night snacking (LNS) in ten body mass index (BMI) categories in a cross-sectional study of 892,578 non-diabetic people aged 40-74 years old who underwent a checkup. BS and LND were more prevalent in men (20.7% and 40.5%, respectively) than women (10.9% and 17.4%), whereas LNS was more prevalent in women (15.0%) than men (12.2%; all p < 0.0001). The overall prevalence of BS increased linearly with increasing BMI. However, when subjects were divided into men and women, the prevalence of BS showed a U-shaped relationship with BMI in men (n = 479,203). When male subjects were restricted to those in their 40s or those reporting LND, the prevalence of BS further increased, maintaining a U-shaped form. Logistic regression analysis also showed a U-shaped relationship in the adjusted odds ratios of BMI categories for BS in men and a J-shaped curve in women. In conclusion, our study revealed an unexpectedly high prevalence of BS in middle-aged low-body-weight men.