Background: Vitamin D is an essential nutrient for bone growth, mineralization, and other metabolic processes in the human body. Hence, insufficiency or deficiency of this vitamin can have long-term effects, particularly for children. Objectives: The aims of this study were to determine the prevalence of vitamin D deficiency in children up to 2 years of age and investigate the independent predictors of vitamin D deficiency. Methodology: This cross-sectional study was conducted among 484 children aged up to two years who were admitted to the hospital for the treatment of any acute condition from January to November 2021. Serum 25(OH)D was used to determine the level of vitamin D. The serum 25(OH)D was categorized into 3 groups: Sufficiency (>30 ng/mL), insufficiency (20–30 ng/mL), and the deficiency (<20 ng/mL). Results: Overall, vitamin D deficiency was observed in 70.5% of the children, of whom 45.9% had insufficient levels, and one-fourth (24.6%) showed deficiency. The children aged 2–12 months (infants) were more likely to be vitamin deficient compared to children aged 12 months and above. The children who lived in urban areas had a threefold increased risk of vitamin D deficiency (aOR = 3.0, 95% CI 1.78–5.08). The children who were exposed to sunlight for less than 3 days per week experienced a higher risk of developing vitamin D deficiency (aOR = 4.17, 95% CI 2.04–10.88). Children who had received only breast milk were more than two times more likely to experience vitamin D deficiency (aOR = 2.42, 95% CI 1.12–5.23) compared to their counterparts. Conclusion: Our study reveals a high prevalence of vitamin D deficiency among children aged up to two years. Infants, urban dwellers, only breastfed, and exposure to sunlight for less than three days per week were identified to be the independent risk factors for vitamin D deficiency. The results of this work call for enhancing awareness to ensure adequate levels of vitamin D for better health of the children in this region of Saudi Arabia.