Background Vitamin D (VD) plays a role in reducing the risk of diseases related to the immune system, including autoimmune diseases, by inhibiting proinflammatory cytokines such as IFN-γ. Children with Down syndrome (DS) are known to have interferonopathy due to trisomy 21 and have lower VD levels. This study aimed to evaluate the VD profile in Indonesian children with DS and its correlation with IFN-γ.Methods This study was conducted from March 2020 to June 2021 at Dr. Soetomo General Hospital, Surabaya. Data on sociodemographic status, milk, fish, and meat consumption, and sun exposure were obtained using a self-report questionnaire. VD and IFN-γ levels were measured using an ELISA kit. The chi-square test, t-test, Mann–Whitney test, and linear and logistic regression analysis were performed, with a significance threshold of p < 0.05.Results Of the 122 participants, 80 children had DS and 42 did not. The median VD levels in the DS and non-DS groups were 31.98 ng/mL and 56.19 ng/mL, respectively. The IFN-γ level was higher in the DS group, but this difference was not statistically significant (122.978 ± 123.420 vs. 100.715 ± 97.137 ng/mL, p = 0.548). Children with DS had lower daily milk consumption (300 cc/day vs. 380 cc/day; p = 0.027), sun exposure (17.5 vs. 150 hours/week; p = 0.000), and weekly meat and fish consumption (1 vs. 4 slices/week; p = 0.000). Daily milk consumption was a significant contributing factor for VD adequacy in the DS group (p = 0.000 [OR = 1.008]). VD levels had a significant role in decreasing IFN-γ levels in the DS group (p = 0.039; R2 = 5.8%).Conclusions VD levels in children with DS are lower than in children without DS. Adequate milk consumption can reduce the risk of autoimmunity through the role of VD in reducing IFN-γ levels in children with DS.