The health and intellectual ability of Filipino children limits the Philippines' capacity to rise from its developing country status to that of a developed one. The present study examined the association of nutritional status (anthropometry, micronutrients), physical fitness, and immune health with Filipino schoolchildren's intellectual ability. Using a cross-sectional design, 166 apparently healthy kindergarten and first grade children whose parents signed consent forms underwent the following tests: Wechsler Preschool and Primary Scale of Intelligence (WPPSI)-IV; anthropometric measurements (weight, height), physical fitness tests, blood tests to assess the following: C-reactive protein; vitamins C, D, riboflavin, and iron; white blood cell count (WBC); Epstein-Barr virus (EBV) infection. Data were collected February to December 2023. Chi-square test and Fisher's exact test were used to determine the association of categorical variables with IQ level; that of continuous variables were assessed using t-test. Multiple linear regression was used to identify nutrition and health factors that contributed to the variance in IQ scores after controlling for Epstein-Barr virus and demographic factors (child age, sex, mother's educational attainment). Results showed that most children (88.8%) tested positive for EBV. Many (52%) had below average IQ. Improved intellectual capacity was associated with sufficient serum vitamin D (p=.036) and higher physical fitness scores (p=.010). Mother's education contributed significantly to the variance in children's overall IQ scores (p=.031), with increasing maternal education predicting higher scores. Under conditions of continuing viral infections, sufficient serum vitamin D and higher physical fitness levels were positively associated with children's intellectual capacity. Maternal education was the strongest predictor of children's overall IQ suggesting the need for educational opportunities for women and girls to improve the quality of the country's human resources.