This study examined whether the distribution of biochemical, physiological, and metabolic risk factors for non-communicable diseases (NCDs) among children and youth in urban India vary by socioeconomic status (SES). Data were derived from a cross-sectional survey of students enrolled in the 2nd and 11th grades in 19 randomly selected schools in Delhi (N = 1329) in 2014-15. Mixed-effect regression models were used to determine the prevalence of risk factors for NCDs among private (higher SES) and government (lower SES) school students. After adjusting for age, gender, and grade we found the percentage of overweight (13.16% vs. 3.1%, p value < 0.01) and obese (8.7% vs. 0.3%, p value < 0.01) students was significantly higher among private relative to government school students. Similarly, significantly higher percentage of private school students had higher waist circumference values (7.72% vs. 0.58%, p value < 0.01) than government school students. Furthermore, similar trend was observed across schools in the distribution of other NCD risk factors: raised blood pressure, raised total cholesterol, and low-density lipoprotein. Surprisingly, despite a higher prevalence of all risk factors, significantly higher percentage of private school students had adequate/ideal levels of high-density lipoprotein. Overall, the risk profile of private school students suggests they are more vulnerable to future NCDs.