Objectives: Iron deficiency (ID) and its anemia (IDA) are the most prevalent nutritional deficiency worldwide. Dysfunction of the autonomic nervous system (ANS) is a consequence of anemia regardless to its type. Many studies found ANS dysfunction in adults with ID/IDA. This study evaluated ANS function in children and adolescents with IDA as related studies are scare. Patients and Methods: This prospective study included 60 children with IDA (boys = 20; girls = 40; age: 14.50 ± 2.04 yrs.). Blood concentrations of hemoglobin, ferritin and iron were determined. ANS function testing were carried twice (at baseline and 3 months after iron therapy). They included measuring of heart rate at rest and its variation (HRV) in response to standing and breathing and blood pressure (BP) changes in response to standing, sustained handgrip and cold. Results: Manifestations of IDA included excessive fatigue, dizziness, palpitation at rest and headache. Children with IDA had significant changes in resting heart rate, blood pressure and HRV parameters compared to healthy mates indicating sympathetic hyperactivity and reduction in parasympathetic activity. Early, definite and severe ANS dysfunctions were found in 20%, 36.67% and 3.33%, respectively. For children with IDA, significant correlations were found between ferritin levels and HB and iron levels (P = 0.001), HRV to active standing, deep breathing and Valsalva maneuver (P = 0.001) and systolic and diastolic (P = 0.001) and diastolic BPs in response to sustained handgrip and cold (P = 0.001). Ferrous sulfate therapy (6 mg/kg/day) for 3 months resulted in improvement of ANS manifestations with IDA. Conclusion: ANS dysfunctions are common consequences of IDA in children and can be attributed to the increased need of tissues for oxygen, resulting in sympathetic hyperactivity. Optimal iron therapy can improve ANS consequences of IDA.