Background Vitamin D deficiency (VDD) and iron deficiency are two common nutritional problems and cause a variety of health issues in children even if they are asymptomatic. The potential relationship between the two remains poorly understood. Propose To study the status of vitamin D in Egyptian young children and its correlation with iron deficiency. Patients and methods This cross-sectional study included 85 apparently healthy Egyptian children between 6 and 9 years old randomly selected from pediatric outpatient clinic of General Port Fouad Hospital, Port Said City, in the period from July to November 2019. A written informed consent was taken from all participants’ parents after proper explanation of the study. All children were subjected to complete history taking, anthropometric measurements, systemic examination, and laboratory investigations, including complete blood count, serum vitamin D level, serum iron, and ferritin level, which were performed for children expected to have iron deficiency through red blood cells indices in complete blood count. Results A total of 85 patients (age, 7.36±1.1 years; male to female ratio was 1 : 1) were classified according to their 25-hydroxyvitamin D levels into three groups: VDD 40% (<20 ng/ml), vitamin D insufficiency 40% (20–29 ng/ml), and vitamin D sufficiency 20% (≥30 ng/ml). Of 24 suspected iron-deficient cases, 80% of them were in the VDD+insufficient vitamin D groups compared with 20% in the sufficient group (P<0.001). Conclusion Among the apparently healthy young Egyptian children, VDD is common with increased risk of iron deficiency. There is a significant positive correlation between vitamin D level and age, hemoglobin, mean corpuscular volume, mean corpuscular hemoglobin, and serum iron levels but not with serum ferritin level. Physicians should therefore ensure that vitamin D levels are evaluated in anemic children and provide adequate supplementation to prevent deficiencies of both nutrients.