Background and Objective: The relationship between food insecurity (FI) and micronutrient intake inadequacies is increasing in young ages. This study investigated the association between children’s FI and micronutrient intake in Brazilian schoolchildren. Methods: This is a cross-sectional representative study conducted with children from the Schoolchildren Health Assessment Survey (PASE, in Portuguese). The sample consisted of 378 children aged 8 to 9 from all the schools in the urban area of Viçosa, Minas Gerais, Brazil, in 2015. The FI was evaluated by the Brazilian Food Insecurity Scale, and the food intake by three 24-hour-recall, being one of a weekend day. The consumption adequacy was performed by the Estimated Average Requirement (EAR) method as a cut-off point. Poisson regression models were adjusted for sex, age, and race. Statistical analyzes were conducted by STATA 14 considering a statistical significance level of 5%. This study was approved by the Human Research Ethics Committee of the Universidade Federal de Viçosa. Results: The majority of our sample were non-white (68.5%), and the mean per capita income was US$ 242.28 ± 276.61. We identified a high prevalence of FI in children (48.4%). The prevalence of intake inadequacy of micronutrients was high as well, such as calcium (81%), iron (35.2%), zinc (47.6%), vitamin D (91.5%), phosphorus (47.9%), sodium (51.9%), copper (35.5%) and magnesium (52.9%). The FI was positively associated with intake inadequacy of calcium (PR: 1.21%; 95%CI: 1.10%; 1.33%), iron (PR: 1.41%; 95%CI: 1.07%; 1.86%), zinc (PR: 1.26%; 95%CI: 1.03%; 1.53%), phosphorus (PR: 1.27%; 95%CI: 1.08%; 1.49%), copper (PR: 1.43%; 95%CI: 1.10%;1.89%), and magnesium (PR: 1.27% (1.08%; 1.51%). Conclusions: The high prevalence of food insecurity and its association with an inadequate intake of micronutrients indicate the need to implement public policies to improve access to micronutrients in children’s diets in developing country as Brazil.