Background: Congenital heart disease (CHD) is the most prevalent congenital abnormality in children. Infants and children with CHD are at a higher risk of malnutrition. Aim: The purpose of this research was to investigate the frequency of anthropometric malnutrition, for example, underweight, wasting, and stunting, among infants and children with CHD attending the emergency room of a large tertiary hospital. Methods: Between January 2022 and August 2022, a cross-sectional study was carried out on 96 infants and children presenting with heart failure at Children's Hospital Cairo University. All enrolled participants had anthropometric and biochemical nutritional assessments. Anthropometric z-scores were calculated for each infant or child using WHO reference ranges. Biochemical and nutritional assessments were carried out through screening for iron deficiency anemia and electrolyte imbalances. Results: Ninety-six infants and children were enrolled in our study, with males representing 54.8%. Seventy percent of the patients were anthropometrically malnourished, with underweight being the most prevalent (59.4%). Some children had more than one type of malnutrition. Electrolyte imbalance was a major biochemical malnutrition indicator, with hypophosphatemia present in 39.6% of the enrolled children. Conclusion: Malnutrition poses a significant health problem in infants and children with CHDs. To improve outcomes, it is essential to integrate systematic measures for identifying and managing malnutrition into the care of these patients. Both anthropometric and biochemical malnutrition should be routinely screened in all clinical settings to ensure comprehensive management and support.