This study aimed to describe the national trends in mean energy and nutrient intakes in Japanese children and adolescents from 1995 to 2019. We used data obtained from the National Health and Nutrition Survey and included 54,871 participants aged 1-19 years. The dietary intake was estimated using a 1-day, semi-weighed, household-based, dietary record. The trends of mean energy and nutrient intakes were analyzed using the Joinpoint Regression Program. A declining trend in the mean energy intake was observed in toddlers aged 1-6 years, school girls aged 7-14 years, and adolescent girls aged 15-19 years, while the mean energy intake from protein, fat, and carbohydrates changed little over time. The mean salt equivalent showed a decreasing trend in all age groups, although the 2019 mean values were above the tentative dietary goal for preventing lifestyle-related diseases, especially in adolescent boys. Declining trends in mean vitamin (vitamin A, vitamin B12, folate, vitamin D, and vitamin K) and mineral (calcium, iron, and copper) intakes were observed, while trends in the mean vitamin B6 and zinc intakes were unchanged since 2001. Continuous monitoring of dietary intake and further research are required to raise awareness of unhealthy diet habits and to improve the food environment for the healthy growth and development of children and adolescents.