ABSTRACT Background Vitamin B12 and folate are essential micronutrients, a deficiency of which causes anaemia, poor growth and an increased risk of infections, along with irreversible neurological damage to the developing brain in children. Methods A hospital-based prospective observational study was conducted in 100 children with severe acute malnutrition (SAM) aged 6–59 months admitted to a tertiary-care facility in northern India from July 2021 to June 2022. A structured proforma was used to record socio-demographic information, a detailed clinical history, results of general and systemic physical examination and a detailed anthropometric assessment. Serum folate and vitamin B12 were estimated by electrochemiluminescence. Results The mean age of the children was 24.18 months, and 64.0% were aged 6–12 months. The male-to-female ratio was 1.08:1. Anaemia was present in 87.0% of the children, and it was severe in 35% of them. There was serum vitamin B12 and folate deficiency in 61.0% and 19.0%, respectively. A deficiency of vitamin B12 was significantly associated with delayed developmental milestones in all domains, a mid-upper-arm circumference of <11.5 cm, severe anaemia, a low platelet count and folate deficiency, and a folate deficiency was significantly associated with older age, delayed developmental milestones in all domains, severe anaemia, a low platelet count and vitamin B12 deficiency. Conclusion Vitamin B12 deficiency is highly prevalent in children aged 6–59 months with SAM, but the prevalence of folate deficiency is much lower. Apart from iron and folic acid supplementation, government programmes should consider vitamin B12 supplementation for children aged 6–59 months.