The influence of free sugars intake on nutrient intake remains unclear in Japanese children and adolescents with relatively low free sugars intake. This cross-sectional study aimed to investigate the relationship between free sugars and selected nutrients intakes using data from the 2016 National Health and Nutrition Survey, Japan, based on the World Health Organization (WHO) recommendations (<5% or <10% of energy [%E]) for free sugars intake. A 1-day weighed dietary record was assessed in Japanese children and adolescents (aged 1-19 years; n = 2,919). Mean intakes for selected nutrients and food groups were compared according to free sugars intake categories (<2.5%E, 2.5 to <5%E, 5 to <10%E, and ≥10%E) with adjustment for sex, age, and weight status. Inverse associations were observed between intakes of free sugars and 21 of 24 micronutrients assessed, except for vitamins A and C and calcium. Significantly reduced intakes were identified for 22 and 14 micronutrients in the ≥10%E and 5 to < 0%E categories, respectively, compared with the lower categories. Mean micronutrients intakes at the <2.5%E category did not differ from those at the 2.5 to <5%E category. Free sugars intake had positive associations with intakes of sugars and jams, confectioneries, fruit and vegetable juices, and soft drinks and negative associations with intakes of pulses and nuts and vegetables. This study showed that nutrient dilution was associated with higher free sugars intake among Japanese children and adolescents. The findings suggest that the WHO recommendations might help prevent nutrient dilution in Japanese children and adolescents.