What is already known on this topic?Iron deficiency (ID) is the most widespread micronutrient deficiency and have several adverse effects on health. Consequences of ID among children include delayed psychomotor development and impaired cognitive performance, which makes it important to monitor the iron status of children.What is added by this report?In this study, the serum ferritin (SF) level was 56.6 (95% CI: 56.0–57.2) ng/mL in 65,293 children aged 6–17 years old in the National Nutrition and Health Surveillance in China in 2016–2017. ID prevalence varied significantly in children stratified by sex, age, and regions ranging from 1.0% to 28.1% judged by the standard of SF<15 ng/mL and SF<25 ng/mL. ID prevalence in females aged 12–17 years was the highest among children aged 6–17 years.What are the implications for public health practice?Understanding iron status of school children could provide evidence and data for developing policies and strategies for ID and iron deficiency anemia (IDA) control and prevention. Females aged 12–17 years showed high ID prevalence, and iron-rich food interventions are strongly recommended.