Based on the data from six Chinese National Surveys on Students Constitution and Health (CNSSCH) from 1985 to 2010, we explored the secular trend in the prevalence of obesity in urban Chinese children over a period of 25 years. The aim of this study was to examine the gender disparities in the prevalence of childhood obesity over time. The standardized prevalence of obesity in Chinese children increased rapidly during the past 25 years from 0.2% in 1985 to 8.1% in 2010. The increasing trend was significant in all age subgroups (p<0.01). Although the prevalence of obesity continuously increased in both boys and girls, the changing pace in boys was faster than that in girls. Age-specific prevalence odds ratios (PORs) of boys versus girls for obesity increased over time during the 25 year period. The prevalence of obesity in boys was significantly higher than in girls in all age-specific subgroups from 1991 and after. The gradually expanding gender disparity suggests the prevalence of obesity in boys contribute to a large and growing proportion of obese children. Therefore, it is critical for developing and implementing gender-specific preventive guidelines and public health policies in China.