We explored the association between the trajectory of the continuous metabolic syndrome score (cMetS) in childhood with high-sensitivity C-reactive protein (hs-CRP) and carotid intima-media thickness (CIMT), which are known to increase cardiovascular disease risk in adolescence. The trajectory of cMetS in childhood (from 3 to 12 years of age) was identified in 833 children who participated in the Ewha Birth and Growth Study. The associations between cMetS and hs-CRP and CIMT were analyzed in 204 out of 833 children who participated in the follow-up at 13–15 years of age and measured hs-CRP and CIMT. Among the 833 children, three groups were classified: cMetS maintained at a low level (n = 198, 23.77%), middle level (n = 530, 63.63%), and at high levels (n = 105, 12.61%). The group with a stable-high cMetS trajectory showed significantly higher hs-CRP levels, and the statistical significance was maintained after adjusting for covariates. This study found that a consistently high cMetS in childhood was significantly associated with higher hs-CRP levels in adolescents, suggesting that it is necessary to intervene in metabolic risk factors early in life to reduce the risk of cardiovascular disease later in life.