Background We aimed to compare the prevalence of childhood obesity and other cardiometabolic risk factors from two independent cohorts (2008 and 2013) in Riyadh, Saudi Arabia. Methods A total of 4549 adolescents aged 12–18 years [2454 boys, 2095 girls], taken from two independent cohorts, 5 years apart (2008 and 2013), were included. Anthropometrics were measured, and fasting blood samples were taken to ascertain glucose and lipid profile. Results The overall prevalence of obesity was significantly higher in 2013 [15.3 (95% confidence interval 13.7–16.9)] than 2008 [12.6 (11.3–13.9)] (P = 0.012). Stratified by sex, the prevalence of obesity among boys was significantly higher in 2013 than 2008 [2008 = 12.0 (10.3–13.7) versus 2013 = 17.4 (15.1–19.7); P < 0.001]. The age groups 13 and 15 years had a significantly higher mean triglycerides in 2013 than 2008 (P‐values 0.003 and <0.001, respectively) and lower mean HDL‐cholesterol also in the 13 years old age group (P < 0.001). Conclusions The prevalence of childhood obesity in Saudi Arabia has increased in particular age groups (13–15 years) during a 5‐year span. Special attention is warranted in these vulnerable age groups, particularly in boys, as cardiometabolic risk factors appear to worsen.