Aim: To assess the dental caries experience in relation to nutritional status among 6–12- year-old school-going children and those with congenital heart disease in Bhubaneswar city. Materials and methods: A cross-sectional study was conducted among 6–12-year-old healthy school-going children and those with congenital heart disease for a period of 6 months (October 2019–March 2020) in Bhubaneswar, India. Type III clinical examination was carried out as per American Dental Association (ADA) specifications using plane mouth mirrors and community periodontal index (CPI) probes. Clinical oral examination and measurement of the weight and height of the child were performed by a single examiner. Data was analyzed using Statistical Package for the Social Sciences (SPSS) version 21.0. Results: The overall mean decayed missing filled primary teeth surfaces (dmfs) in primary dentition was higher (5.93 ± 10.224) in subjects with congenital heart disease (CHD) (group I) than in healthy controls (3.41 ± 6.192). The overall mean decayed missing filled permanent teeth surfaces (DMFS) in permanent dentition was 0.33 ± 1.105 in subjects with CHD (group I) and 0.24 ± 0.714 in group II. In group I, the majority of them (58.9%) were underweight, followed by 41.1% who were a healthy weight. However, in group II, 47.9% of the study subjects were healthy weight, 26.1% were underweight, 14.4% were obese, and 11.7% were overweight. Conclusion: This study concluded that children with CHD have a higher dental caries experience and poor nutritional status as compared to healthy school-going children.