An unhealthy diet during childhood directly impacts the risk of developing noncommunicable diseases (NCDs) later on in life. However, well-documented information on this issue is lacking. We investigated the dietary quality of young Indonesian children and assessed the relationship to serum adiponectin levels as an early marker of NCDs. Eighty-five (44 girls and 41 boys) Indonesian preschool-age children in East Jakarta were included in this study. Dietary intake data were gathered by collecting repeated 24-hour recalls for one weekday and one day during the weekend, which were then further converted into participants' Healthy Eating Index (HEI) 2015 scores. Meanwhile, an enzyme-linked immunosorbent assay was performed to determine the serum adiponectin level. A multiple regression analysis was performed to assess the association between the HEI 2015 score and serum adiponectin, adjusting for potential confounders. The mean HEI 2015 score was 33.2 ± 8.3 points, which was far below the recommended score of ≥ 80 points, while the mean serum adiponectin was 10.3 ± 4.1 μg/mL. Multiple linear regression testing showed that a one-point increase in the HEI 2015 score was significantly associated with an increase in the serum adiponectin level by 0.115 μg/mL after adjusting for exclusive breastfeeding history (β = 0.115; 95% CI = 0.010-0.221; p = 0.032). In conclusion, better adherence of young children to a healthy diet has a positive association with their adiponectin level. This result suggests that strengthening children's dietary quality from an early age by involving all parties in the children's environment (e.g., parents, teachers at school, policymakers) may help to reduce the risk of NCDs later on in childhood and during adult life.