Nutritional inadequacy has been a major health problem worldwide. One of the many health problems that result from it is anemia. Anemia is considered a health concern among all ages, particularly children, as it has been associated with cognitive and developmental delays. Researchers have investigated the association between nutritional deficiencies and anemia through various methods. As novel analytical methods are needed to ascertain the association and reveal indirect ones, we aimed to classify nutritional anemia using the cluster analysis approach. In this study, we included 4,762 students aged between 10 and 17 years attending public and UNRWA schools in the West Bank. Students' 24-h food recall and blood sample data were collected for nutrient intake and hemoglobin analysis. The K-means cluster analysis was used to cluster the hemoglobin levels into two groups. Vitamin B12, folate, and iron intakes were used as the indicators of nutrient intake associated with anemia and were classified as per the Recommended Dietary Allowance (RDA) values. We applied the Classification and Regression Tree (CRT) model for studying the association between hemoglobin clusters and vitamin B12, folate, and iron intakes, sociodemographic variables, and health-related risk factors, accounting for grade and age. Results indicated that 46.4% of the students were classified into the low hemoglobin cluster, and 60.7, 72.5, and 30.3% of vitamin B12, folate, and iron intakes, respectively, were below RDA. The CRT analysis indicated that vitamin B12, iron, and folate intakes are important factors related to anemia in girls associated with age, locality, food consumption patterns, and physical activity levels, while iron and folate intakes were significant factors related to anemia in boys associated with the place of residence and the educational level of their mothers. The deployment of clustering and classification techniques for identifying the association between anemia and nutritional factors might facilitate the development of nutritional anemia prevention and intervention programs that will improve the health and wellbeing of schoolchildren.