The influence of free sugar intake on nutrient intake remains unclear in Japanese children and adolescents with relatively low free sugar intake. This cross-sectional study aimed to investigate the relationship between free sugar and selected nutrient intakes using data from the 2016 National Health and Nutrition Survey, Japan, based on the WHO recommendations (<5 % or <10 % of energy (%E)) for free sugar intake. A 1-d weighed dietary record was assessed in Japanese children and adolescents (aged 1–19 years; n 2919). Mean intakes for selected nutrients and food groups were compared according to free sugar 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 twenty-one of twenty-four micronutrients assessed, except for vitamins A and C and Ca. Significantly reduced intakes were identified for twenty-two and fourteen micronutrients in the ≥10 %E and 5 to <0 %E categories, respectively, compared with the lower categories. Mean micronutrient intakes at the <2·5 %E category did not differ from those at the 2·5 to <5 %E category. Free sugar 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 sugar intake among Japanese children and adolescents. The findings suggest that the WHO recommendations might help prevent nutrient dilution in Japanese children and adolescents.