Background: ‘Vitamin D deficiency is a prevalent global health issue, particularly in children with chronic illnesses. Despite its essential role in bone health, immunity, and growth, this deficiency remains under-recognized in vulnerable populations, including those with chronic conditions’. Limited local data exists on its ‘prevalence and associated risk factors’ in children in Pakistan. To determine the prevalence of vitamin D deficiency in children with chronic illnesses and identify associated demographic, clinical, and environmental risk factors’. Methods: This cross-sectional study was conducted at Muhammad College of Medicine, Peshawar, from January 2023 to January 2024. A total of 101 children aged 1–16 years with chronic illnesses were included. ‘Serum 25 hydroxyvitamin D (25(OH)D) levels were measured, and data on demographics, sunlight exposure, dietary habits, and clinical conditions were collected’. Vitamin D deficiency was defined as serum 25(OH)D levels below 20 ng/mL. Statistical analyses were performed to identify significant associations. Results: ‘The prevalence of vitamin D deficiency was’ 65.3%. ‘Children aged 5–10 years’ exhibited the highest deficiency rates (44.6%), followed by those >10 years (30.7%) and <5 years (24.8%) (P=0.032). Significant risk factors included low socioeconomic status (P=0.041), limited sunlight exposure (<2 hours/week, P=0.015), urban residency (P=0.018), and chronic illnesses such as asthma ‘(P=0.027) and chronic kidney disease’. Vitamin D supplementation was a protective factor (P=0.002). Family history of deficiency and exposure to second-hand smoke were also significantly associated with deficiency. Conclusion: Vitamin D deficiency is highly prevalent in children with chronic illnesses, with multiple modifiable risk factors identified. Targeted interventions, including increased sunlight exposure, dietary improvements, and routine supplementation, are essential to address this health concern.