Background Since there is no evidence demonstrating the relationship between dietary patterns and subclinical atherosclerosis in children and adolescents, we aimed to examine the association between dietary patterns and carotid intima-media thickness (cIMT) in children and adolescents with overweight and obesity. Methods Data were collected on individuals, aged 6–13 years (n = 339) recruited from primary schools with age- and sex-specific body mass index (BMI) Z-score > 1, based on WHO criteria. Dietary intake was assessed using a valid and reliable food frequency questionnaire and dietary patterns were derived by factor analysis. Measurement of cIMT was performed by means of ultrasonography for the wall of common carotid artery. Results The mean ± SD age, BMI Z-score and cIMT of study participants were 9.3 ± 1.7 years, 2.5 ± 0.7 and 0.403 ± 0.057 mm, respectively. Three dietary patterns were identified, which accounted for 23.0% of the total variance, including the healthy, the traditional, and the unhealthy patterns. After adjusting for age, sex, pubertal status, smoking exposure, physical activity, body fat percentage, and intake of magnesium and energy, a significant inverse association was observed between the healthy dietary pattern and cIMT (β = − 0.131, P = 0.019), whereas none were found between cIMT and the traditional (β = − 0.004, P = 0.932) and the unhealthy dietary (β = 0.004, P = 0.942) patterns. Conclusions Results of the present study indicate that adherence to healthy dietary pattern could prevent increased cIMT in children and adolescents with overweight and obesity. Further cohort design research is required to elucidate the association between dietary patterns and cIMT in children and adolescents.