Vitamin A deficiency (VAD) remains a major health issue in developing nations, contributing to preventable childhood blindness. However, there is lack of recent data on xerophthalmia, especially among school-aged children in Malaysia. We hypothesized that xerophthalmia persists among rural schoolchildren in Malaysia and potentially associated with socio-demographic status and malnutrition. We conducted a cross-sectional study on 596 schoolchildren (8-12 years) from ten rural primary schools located in five states across Malaysia. Children meeting the criteria for xerophthalmia assessment included those diagnosed with vitamin A deficiency (VAD) (plasma retinol < 0.70 µmol/L) and marginal VAD (plasma retinol 0.70 to < 1.05 µmol/L). The overall prevalence of xerophthalmia was 48.8%, with the most common ocular sign being conjunctival xerosis (38.9%). The occurrence of xerophthalmia was negatively associated with retinol-binding protein 4 (RPB4) (P=0.003), alpha-carotene (P=0.04), hemoglobin (P=0.004), weight (P=0.02), body mass index (BMI) (P=0.04) and WAZ (weight-for-age z-score) (P=0.04) status. Based on multivariate logistic regression analysis, a higher risk of xerophthalmia was observed in boys (Adjusted odd ratio [AOR]: 1.7, 95% confidence interval [CI]: 1.2-2.5) and Orang Asli (OA, indigenous) schoolchildren (AOR: 2.0, 95% CI: 1.3-3.0), while schoolchildren with overweight/obesity status (AOR: 0.5, 95% CI: 0.3-0.8) were associated with a reduced risk of xerophthalmia. The present study unveils a high prevalence of xerophthalmia among vitamin A-deficient primary schoolchildren in rural areas of Malaysia, especially among the indigenous community. The identified socio-demographic and nutritional factors associated to xerophthalmia would facilitate the implementation of more targeted interventions in addressing these issues.