Aim Iron deficiency anemia (IDA) is common in the pediatric population and often accompanied by mild thrombocytosis, but rarely profound thrombocytopenia is seen. We describe the data of children with IDA and thrombocytopenia in two centers and discuss the published data in the literature. Methods In this retrospective case series, the medical records of patients under the age of 19 years old diagnosed with IDA in two tertiary medical centers over the last 10 years, were reviewed. The data were collected and compared to the data published in the medical literature. Results All the patients presented with severe IDA and thrombocytopenia improved with iron treatment. Although none of the patients had signs of major bleeding, the thrombocytopenia could mostly be classified as severe (platelet count <50×10E9/L). Due to the severity of the anemia, in about half of the cases, a red blood cell transfusion was given. The peak of the platelet count was seen in the first month after the start of iron treatment. In eight cases of children with IDA, the thrombocytopenia appeared after the supplementation of iron was started. Conclusion Clinically stable children with severe IDA and thrombocytopenia, where other causes are very unlikely, warrant an empiric monotherapy with iron to prevent unnecessary investigations and treatments.