Background: The Mid-Day Meal Program plays a pivotal role in enhancing the nutritional status and educational outcomes of primary school children in India. This study investigates the program’s impact on the nutritional well-being of children across three districts in Bihar. Methods: A community-based cross-sectional study was conducted, involving 1,070 primary school children from Saran, Muzaffarpur, and Patna districts. The assessment of nutritional status was based on indicators such as BMI for age, weight for height, and weight for age. Data related to children’s participation in the Mid-Day Meal Program was collected through relevant questionnaire and analysed using descriptive statistics. Results: Patna has the highest percentage of children receiving mid-day meal (89.86%) with lowest prevalence of wasting and severe wasting. The prevalence of stunting or wasting were more common in children aged greater than 10 years. The analysis revealed substantial challenges in nutritional status, with a high prevalence of stunting, underweight, and wasting among primary school children in the surveyed districts. In contrast, promising trends were observed in terms of menu changes and vegetable inclusion within the Mid-Day Meal Program. Conclusion: The study highlights the pressing need for targeted interventions to address prevalent nutritional issues and improve the program’s impact. These findings provide valuable insights for policymakers and stakeholders to enhance the well-being of primary school children in the region through the Mid-Day Meal Program.