Background: Childhood obesity is an emerging global public health challenge. Evidence for the transition in nutrition in Indo-Asian developing countries is lacking. We conducted these analyses to determine the trends in nutritional status of school-aged children in urban Pakistan. Methods: Data on the nutritional status of children aged 5 to 14 years from two independent population-based representative surveys, the urban component of the National Health Survey of Pakistan (NHSP; 1990-1994) and the Karachi survey (2004-2005), were analysed. Using normative data from children in the United States as the reference, trends for age- and gender-standardised prevalence (95% CI) of underweight (more than 2 SD below the weight-for-age reference), stunted (more than 2 SD below the height-for-age reference) and overweight and obese (body mass index (BMI) 85th percentile or greater) children were compared for the two surveys. The association between physical activity and being overweight or obese was analysed in the Karachi survey using logistical regression analysis. Results: 2074 children were included in the urban NHSP and 1675 in the Karachi survey. The prevalence of underweight children was 29.7% versus 27.3% (p = 0.12), stunting was 16.7% versus 14.3% (p = 0.05), and prevalence of overweight and obese children was 3.0 versus 5.7 (p<0.001) in the NHSP and Karachi surveys, respectively. Physical activity was inversely correlated with being overweight or obese (odds ratio, 95% CI, 0.51, 0.32-0.80 for those who engaged in more than 30 minutes of physical activity versus those engaged in less than 30 minutes' activity). Conclusions: Our study highlights the challenge faced by Pakistani school-aged children. There has been a rapid rise in the number of overweight and obsese children despite a persistently high burden of undernutrition. Focus on prevention of obesity in children must include strategies for promoting physical activity.