The association between breakfast quality and total diet quality of children and adolescents ((1–17.9 years (n = 1570)) from the National Dietary Survey on the Child and Adolescent Population in Spain (ENALIA) was analyzed. Dietary information was collected using two non–consecutive one–day food diaries (1–10 years old) or two 24 h dietary recalls (>10 years). Breakfast quality index (BQI) and a variant of Nutrient Rich Foods index (NRF9.3) were calculated to assess the total diet quality. Children and adolescents who had breakfast on at least one day (n = 1561) were divided into two groups according to BQI: Worse Quality Breakfast (WQB) (BQI < 4 points (P66), n = 781) and Good Quality Breakfast (GQB) (BQI ≥ 4, n = 780). Younger children and those whose parents have university education presented higher BQI. GQB group had significantly higher intakes of micronutrients (vitamins A, D, C, B1, B2, B6, niacin, folate, calcium, potassium, magnesium). Fewer GQB children exceeded the Acceptable Macronutrient Distribution Range for fat and had folate and calcium intakes below their estimated average requirement. Daily NRF9.3 was 496.2 ± 54.0, being higher in GQB (503.8 ± 50.6 vs. 488.6 ± 56.2, p < 0.001). Increasing the quality of breakfast increased the possibility of having a NRF9.3 higher than P50 (OR: 1.893, CI: 1.549–2.315, p < 0.0001). Breakfasts have room for quality improvement in a high percentage of children. A higher quality breakfast is associated with a benefit in the quality of the total diet.