A hospital-based cross-sectional study involving children aged 2–15 years attending the obesity clinic of a tertiary care hospital from January 2016 to March 2018 was carried out to study carotid intima media thickness (cIMT) and its association with cardiometabolic risk factors in children with overweight and obesity. Secondary objective was to compare children with elevated (EcIMT) and normal cIMT (NcIMT). Out of 223 patients enrolled for the study, 102 (45·7 %) had EcIMT. Mean cIMT of the study participants was 0·41 (sd 0·13) mm. Median alanine transaminase levels (27 v. 24, P= 0·006) and proportion of patients with fatty liver (63·7 % v. 48·8 %, P= 0·025) and ≥ 3 risk factors (80·4 % v. 66·1 %, P= 0·003) were higher in the EcIMT group compared with NcIMT group. Proportion of patients with hypercholesterolemia (36·4 % v. 16 %, P= 0·024), elevated LDL-cholesterol (38·6 % v. 16 %, P= 0·013), low HDL-cholesterol (40·9 % v. 20 %, P= 0·027) and dyslipidemia (84·1 % v. 58 %, P= 0·006) was higher in the pubertal EcIMT group and those with fatty liver (63·8 % v. 45·1 %, P= 0·034) was higher in the prepubertal EcIMT group compared with pubertal and prepubertal NcIMT groups, respectively. No significant correlations were observed between cIMT and various cardiometabolic parameters. Our finding of EcIMT in nearly half of the study participants including young children is very concerning as these children are at increased risk of atherosclerotic CVD in adulthood. Interventions starting at a young age are important when trajectories are likely to be more malleable and adverse cardiometabolic phenotypes and subclinical atherosclerosis are reversible.