Breakfast, an important meal of day's menu refills the supply of glucose for metabolism and provides other essential nutrients to keep the energy levels boosted all throughout the day. School children are more prone to skip their breakfast and are vulnerable for their nutritional status and cognitive functioning. In India, 50% of the children population are regular breakfast skippers. To assess the effect of skipping breakfast and its effect on Intelligent Quotient (IQ) level, understanding reasons for skipping breakfast and to study their dietary intake and impart nutrition education. A total of 80 Subjects were selected from both of government and private schools. Data was collected using pre-structured questionnaire and anthropometric measurements along with IQ test and are recorded. Data was entered and analysed using SPSS 16. Reason for skipping breakfast was lack of time among private school children and in government school it was a family practice. Skipping breakfast had resulted in low IQ level and poor academic performance in both the school groups. Breakfast skippers in private school were more prone to overweight but in government school skippers were more prone to underweight. Skipping breakfast has a negative impact on nutritional status of school children effecting their cognitive functioning. And there is a significant association with their IQ level and academic performance.