Background: Obesity is an emerging problem in Pakistan. The authors sought to determine prevalence of obesity and malnutrition in school-going children, from grades 6th to 8th of different schools of Karachi and assess associations that affect the weight of the children. Methodology/Principal Findings: A cross sectional study design with children studying in grades 6th to 8th grade, in different schools of Karachi. We visited 10 schools of which 4 consented; two subsidized government schools and two private schools. A questionnaire was developed in consultation with a qualified nutritionist. Height and weight were measured on calibrated scales. A modified BMI criterion for Asian populations was used. Data was collected from 284 students. Of our sample, 52% were found to be underweight whereas 34% of all the children were normal. Of the population, 6% was obese and 8% overweight. Of all obese children, 70% belonged to the higher socio-economic status (SES) group, while of the underweight children, 63.3% were in the lower SES. Amongst obese children in our study, 65% ate meat every day, compared to 33% of normal kids. Conclusion: Obesity and undernutrition co-exist in Pakistani school-children. Our study shows that socio-economic factors are important since obesity and overweight increase with SES. Higher SES groups should be targeted for overweight while underweight is a problem of lower SES. Meat intake and lack of physical activity are some of the other factors that have been highlighted in our study.