Eating frequency has been associated with nutrient intake and diet quality. The aim of this study was to examine the association between daily nutrient and food group intake and consumption of breakfast and/or snacks among young Japanese adults, as secondary analysis of the 2012 National Health and Nutrition Survey in Japan involved 1420 men and 1659 women aged 20–39 years. Dietary intake data were collected using a one-day semi-weighed household dietary record. Participants were classified into four groups based their breakfast and snack consumption, defined as the consumption of any food or beverage that contained energy based on participant-defined eating occasions; both breakfast and snack consumption (B+S+), breakfast consumption without snacking (B+S–), breakfast skipping and snack consumption (B–S+) and breakfast skipping without snacking (B–S–). The proportion of breakfast skippers among men and women was 11·8 % and 6·6 %, whereas that of snack consumers among men and women was 55·3 % and 68·2 %, respectively. Energy, Mg potassium (in both sexes), vitamin B2, Ca, (only men) and folate and dietary fibre (only women) intakes were higher among breakfast and snack consumers than in the B+S– group. The nutrient intake level of the B+S– group was similar to that of the B–S+ group, whereas the B–S– group had lower energy (both sexes), Cu, dietary fibre and potassium (only women) intakes than the B+S– group. Snack consumption could supplement nutrients that may not be adequately consumed by three meals among young Japanese adults.