Background: Febrile seizure bring on fear to parent because of the recurrence risk and incidence of epilepsy in the future. Many research had been done to identify the association between iron deficiency anemia with febrile seizure but they showed contradictory result. This study was done to compare the incidence of iron deficiency anemia in the group of children with febrile seizure and group of children without febrile seizure. Methods: A case control study was conducted on 160 children aged 18 – 60 months that hospitalized at PKU 1 Muhammadiyah Yogyakarta Hospital during the period of 2010 - 2014. Levels of Erythrocytes, Hemoglobin, Mean Corpuscular Volume and Menzter Index was used to diagnose iron deficiency anemia. Data were analyzed by Chi-Square test to determine differences in the incidence of iron deficiency anemia in the group of children with febrile seizure and group of children without febrile seizure. Odds ratios were estimated by logistic regression on SPSS. Result: Three children (1,86%) in case group experiencing iron deficiency anemia compared to 2 children (1,2%) in the control group (p=0,68). Odd Ratio for iron deficiency anemia in children with febrile seizure was 1,52 (CI 95%, 0,25 – 9,33) compared to children without febrile seizure. Conclusion: There was no statistically difference between children with iron deficiency anemia and without iron deficiency anemia in febrile seizure children