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Micronutrient deficiencies (MNDs) in school-aged children are still a major health problem in Indonesia. This study was designed to examine the status of micronutrients and their relationship to the nutritional status of children aged 5–12 years since an up-to-date database on the micronutrient status of children aged 5–12 years is needed. Data from the 2018 Indonesian Basic Health Research (Riskesdas) were used in this study, with 2456 subjects for analysis. Micronutrient analysis was carried out, including iron status (ferritin, C reactive protein (CRP)), levels of zinc, vitamin D, calcium, and vitamin A (retinol) in school-aged children (5–12 years). The ELISA measurement was applied to measure CRP, ferritin, and vitamin D. Zinc levels were analysed with atomic absorbance spectroscopy (AAS). Moreover, high-performance liquid chromatography (HPLC) was applied to calculate vitamin A. In addition, stunting and thinness data were also obtained from the Riskesdas study. The results showed that the prevalence of stunting and thinness in school-aged children was 11.4% and 9.2%, respectively, showing that the stunting prevalence in the city was lower than in the village (4.5% vs. 6.9%, P = 0.000, respectively). In addition, the prevalence of MNDs in Indonesian children was 13.4%, 19.7%, 4.2%, 3%, and 12.7% for ferritin, zinc, calcium, vitamin A, and vitamin D, respectively. The mean serum level of vitamin A and zinc was significantly lower in stunted children compared to normal school children (P = 0.010 and P = 0.014). The serum concentration of vitamin D was significantly lower in overweight children compared to thin and normal children (P = 0.000). Serum values of ferritin, zinc, and vitamin A were significantly higher in overweight children compared to thin and normal children (P = 0.000). A poor correlation was observed between the z-score of height-for-age (HAZ) and the levels of zinc (r = 0.089, P = 0.000), vitamin A (r = 0.105, P = 0.000), and vitamin D (−0.073, P = 0.000). In addition, very weak correlations between z-scores of body mass index-for-age (BAZ) and the serum concentrations of ferritin (0.091, P = 0.000), zinc (r = 0.115, P = 0.000), vitamin A (r = 0.137, P = 0.000), and vitamin D (r = −0.112, P = 0.000) were also seen. In conclusion, school-aged children in Indonesia experienced stunting, thinness, and micronutrient deficiency. Furthermore, stunting and thinness were also related to micronutrient deficiencies.