School-going children and adolescents are rarely targeted in nutrition surveys, despite the significant impact of nutritional status on their health, cognition, educational achievements and future economic productivity. The present secondary data analysis evaluated the nutritional status of children and adolescents in the 5–18 years age group. The anthropometric measurements of children and adolescents studying in the government and government-aided schools were collected under the ‘Rashtriya Bal Swasthya Karyakram’ in the District Fatehgarh Sahib of Punjab, India between March and August 2018. It was analyzed using SPSS version 21. Mean and standard deviation for weight-for-age, height-for-age, body mass index (BMI) for age z-scores were calculated using World Health Organization’s Anthro-plus software. A total of 897 children’s data were included in the study. Out of 352 children in 5–9 years age group, mean weight, height and BMI were 15.7 ± 3.8 kg, 110.7 ± 10.6 cm and 12.7 ± 2.1 kg/m². About 58.8%, 37.4% and 31.8% of the children were categorized as severely underweight, stunted and thin, respectively. In the 10–18 years age group, mean weight, height and BMI were 30.5 ± 9.5 kg, 140 ± 13.4 cm and 15.2 ± 2.6 kg/m². Severe stunting was present in 19.4% of adolescents, while 26.9% were severely thin. Our study depicts a high level of undernutrition in school-going children and adolescents. There is a need to strengthen the nutrition interventions for middle childhood and adolescence period that can help in a healthy transition from childhood to adulthood and break the intergenerational cycle of malnutrition. Lay summary National and state-level health-priorities focus mainly on improving the nutrition status of under-5-year children, while the school-going children and adolescents are usually neglected. The present secondary data analysis estimates the burden of malnutrition in school-going children and adolescents. These data were collected under one of India's national health programs that intend to tackle childhood illnesses. Our study depicts a high level of undernutrition in school-going children and adolescents. We found that girls were affected more by malnutrition in middle childhood, i.e. during 5–9 years (both by stunting and thinness) compared to boys. But in middle and late adolescence, males were more stunted and thin compared to females. Programs to support adolescents' nutrition interventions could provide an opportunity for a healthy transition from childhood to adulthood and could be an essential step in breaking the intergenerational cycle of malnutrition.