Evidence on the association of vitamin D and parathyroid hormone (PTH) with cardiovascular risk factors in the young is limited. We therefore assessed the relationships of circulating vitamin D and PTH concentrations and subclinical atherosclerosis in overweight or obese children and adolescents. This was a cross-sectional study, investigated the association of 25-hydroxyvitamin D (25(OH)D), intact PTH (iPTH), and iPTH/25(OH)D ratio with carotid intima-media thickness (cIMT) in 368 Iranian children and adolescents with a body mass index (BMI) ≥1 z-score based on WHO criteria. Ultrasound measurement of cIMT was performed. Multivariable linear and logistic regressions were used to test associations between 25(OH)D, iPTH, and iPTH/25(OH)D ratio using one-ln-unit increment with cIMT. Median (25-75 interquartile range) 25(OH)D and iPTH concentrations were 11.8 (8.2-18.6) ng/ml and 38.2 (25.0-61.4) pg/ml, respectively. Among boys, each one-ln-unit increase of iPTH and iPTH/25(OH)D ratio was significantly associated with 0.194 mm and 0.147 mm increase, respectively, in cIMT, after adjustment for confounders. A similar pattern of association was observed between iPTH (β = 0.143, p = 0.037) and iPTH/25(OH)D ratio (β=0.172, p = 0.007) with cIMT among obese participants. Furthermore, among obese participants in the fully adjusted model, each one-ln-unit increase of iPTH and 25(OH)D/iPTH ratio was significantly associated with 53% and 39% increased odds of having high cIMT, respectively. Girls and those who were overweight did not show any significant association of 25(OH)D, iPTH, and iPTH/25(OH)D ratio with cIMT. High iPTH and iPTH/25(OH)D ratio were associated with increased cIMT in boys and those who are obese.