Food insecurity is a public health concern that affects children worldwide, yet it represents a particular burden for low- and middle-income countries. This study aims to utilize machine learning to identify the associations between food insecurity and nutrient intake among children aged 5 to 18 years. The study’s sample encompassed 1040 participants selected from a 2022 food insecurity household conducted in the West Bank, Palestine. The results indicated that food insecurity was significantly associated with dietary nutrient intake and sociodemographic factors, such as age, gender, income, and location. Indeed, 18.2% of the children were found to be food-insecure. A significant correlation was evidenced between inadequate consumption of various nutrients below the recommended dietary allowance and food insecurity. Specifically, insufficient protein, vitamin C, fiber, vitamin B12, vitamin B5, vitamin A, vitamin B1, manganese, and copper intake were found to have the highest rates of food insecurity. In addition, children residing in refugee camps experienced significantly higher rates of food insecurity. The findings emphasize the multilayered nature of food insecurity and its impact on children, emphasizing the need for personalized interventions addressing nutrient deficiencies and socioeconomic factors to improve children’s health and well-being.