Anemia affects approximately 30% of children all over the world. Acute respiratory tract infections (ARTI), urinary tract infections (UTI) and gastroenteritis (GE) are common infectious entities in children. Here, we assessed the association between anemia and development of recurrent ARTI, UTI, and GE in children. This was a case-control study in hospitalized 2–5 years old children in Professorial Pediatric Unit at Teaching Hospital Anuradhapura, Sri Lanka. An 18-month follow up was done to assess the risk factors for the development of recurrent ARTI, GE, UTI, and control presented without infections. Further, 6-month follow up done after 3-month iron supplementation to assess the occurrence of recurrences. Blood Hb concentration was measured using Drabking’s reagent. Logistic regression was used to find the risk factors for the development of recurrences. In ARTI, 121/165 (73.3%), GE, 88/124 (71%), UTI 46/96 (47.9%) and control 40/100 (40%) were having anemia. Initial ARTI group, recurrent ARTI was 24 (14.5%, p = 0.03); initial GE group: recurrent GE was 14 (11.3%, p = 0.03), recurrent ARTI was 11 (8.9%, p = 0.04); initial UTI group, development of; recurrent UTI was 8 (8.3%, p = 0.04); control, recurrent ARTI was 11 (11%, p = 0.03). Following 3-month iron supplementation reduction of recurrences was significant: initial ARTI recurrent ARTI in 90%, recurrent GE in 77.7%; initial GE recurrent GE in 83.3%, recurrent ARTI in 80%; initial UTI recurrent ARTI in 71.4% and control recurrent ARTI in 88.8%. Iron deficiency is a major type of anemia and anemic children are more prone to develop recurrent ARTI and GE. Once iron deficiency being corrected the rate of recurrent ARTI and GE was reduced. This would be a boost for policy developers to implement strategies at the community level to prevent iron deficiency in children to reduce ARTI and GE recurrences.