Around one-quarter of the world’s children suffer from iron deficiency anemia, and many of them live in malaria-endemic areas. However, there is evidence that iron supplements can increase risk of severe malaria morbidity. The dilemma is how to move forward with interventions to prevent iron deficiency and its consequences in young children, using strategies that minimize risks of malaria and related infections. Screening for iron deficiency is problematic for several reasons. Two complementary strategies are suggested for moving forward with interventions to prevent iron deficiency in children exposed to malaria. The first is to reduce exposure to iron in the form of supplements by: adopting a lifecycle approach to pediatric iron deficiency beginning in utero, using the lowest adequate dose, and giving iron in or with foods. The second is to coordinate iron interventions with malaria control efforts. To stop all iron interventions in malaria-endemic areas is an unreasonable policy option. While research findings continue to increase our understanding, there are also programmatic ways forward with the knowledge at hand.