Background Sickle cell disease (SCD) and iron deficiency anemia (IDA) are significant global health concerns, particularly in pediatric populations. This study investigates the prevalence, clinical impact, and management challenges of IDA in children with SCD. Methods A prospective observational study was conducted at the Department of Pediatrics, Jawaharlal Nehru Medical College(JNMC) and Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi, from June 2022 to May 2024. The study included 60 children diagnosed with SCD. Comprehensive assessments were performed, including medical histories, physical examinations, and hematological investigations. Diagnosis of IDA was based on hemoglobin levels, mean corpuscular volume (MCV), red cell distribution width (RDW), peripheral blood smears, serum iron levels,and serum ferritin concentrations. Results Of the 60 participants, 15% exhibited iron deficiency. No significant gender differences were found in iron deficiency status. A significant association was observed between SCD type and the presence of pallor (p = 0.025) and sickle cell crises (p = 0.023). The study also found no significant association between SCD type and the presence of organomegaly (p = 0.079) or iron deficiency status (p = 0.675). The mean hemoglobin levels varied across SCD types, with sickle cell anemia patients showing lower levels than those with sickle cell trait or disease. Conclusion Diagnosing and managing IDA in children with SCD is complex due to overlapping hematological features and the risk of iron overload from frequent transfusions. Tailored diagnostic and therapeutic approaches are essential to improving hemoglobin levels, reducing complications, and enhancing the quality of life for affected children. This study provides valuable insights for refining clinical practices and emphasizes the need for a multidisciplinary approach to managing these intertwined conditions.