We assessed breakfast in Japan using data from the 2012 National Health and Nutrition Survey. Dietary data were obtained from 1444 children (aged 6–11 years), 1134 adolescents (aged 12–17 years), 6531 younger adults (aged 18–49 years), and 13,343 older adults (aged ≥ 50 years), using a one-day weighed dietary record. Overall, 97% of participants reported consuming breakfast. Compared with breakfast skippers, breakfast consumers had a higher daily diet quality score assessed by the Nutrient-Rich Food Index 9.3 (NRF9.3). For those who consumed breakfast, breakfast accounted for 20–25% of daily energy intake. In comparison with the contribution to energy, breakfast accounted for higher proportions of carbohydrate and riboflavin, and lower proportions of MUFA, n-3 PUFA, thiamin, and niacin, as well as vitamins B-6 and C. The overall diet quality (NRF9.3 score) was positively associated with breakfast intake of protein, n-6 PUFA, n-3 PUFA, carbohydrate, dietary fiber, and almost all micronutrients examined, and inversely with that of added sugar. For foods, the NRF9.3 score was positively associated with breakfast intake of rice, potatoes, pulses, vegetables, fruits, and eggs and inversely with that of bread, sugar, and soft drinks. The findings will be useful in developing dietary recommendations for a balanced breakfast among Japanese.