Skipping breakfast has been reported to decrease daily energy and nutrient intake. We aimed to investigate whether habitual breakfast intake frequency is associated with fat-free mass (FFM) in healthy young subjects. We hypothesized that skipping breakfast and the subsequent negative energy balance may be risk factors for reduced muscle mass. This cross-sectional study included 270 healthy young subjects (152 men, 118 women). We collected information on habitual breakfast intake frequency, sleep quality according to the Pittsburgh Sleep Quality Index, circadian rhythm type using the Morningness-Eveningness Questionnaire, and physical activity using the International Physical Activity Questionnaire. According to the definition of National Health and Nutrition Examination Survey in Japan, the subjects were asked to report habitual breakfast intake frequency over the preceding month (excluding consumption of tablets, energy drinks, confectionary, fruits, dairy products, or sweetened beverages alone). FFM was assessed using dual-energy x-ray absorptiometry; then, appendicular FFM (AppFFM) was calculated. We also calculated appendicular skeletal muscle mass index (kg AppFFM/m2) and %AppFFM (% body weight) to adjust body size between individuals. Multiple regression analysis showed that habitual breakfast intake frequency was positively associated with appendicular skeletal muscle mass index (β = .087, P = .031) and %AppFFM (β = .086, P = .045) after adjusting for age, sex, living conditions, Pittsburgh Sleep Quality Index, Morningness-Eveningness Questionnaire, and International Physical Activity Questionnaire scores as covariates. These findings suggest that skipping breakfast is a risk factor for lower muscle mass in healthy young subjects, irrespective of strong confounders, such as age, sex, and physical activity.