Children with diabetes mellitus (DM) type 1 may be at risk for iron deficiency (ID) although this has been little studied. ID is either an absolute (depleted iron stores) or a functional (restricted iron stores due to chronic inflammation) deficiency each requiring a different therapeutic approach. Unfortunately, absolute ID is often not distinguished from functional ID. Furthermore, iron-deficient anemia may influence hemoglobin A1c (HbA1c) levels.We aimed to determine the prevalence and type of ID and investigate its association with HbA1c levels in pediatric DM type 1 patients. We performed a two-center prospective observational study in which the iron status of Dutch children with DM type 1 was determined during a regular check-up. Absolute ID and functional ID were found in 13/227 (5.7%) and 100/214 (47%) patients, respectively, while only 15/113 (13%) patients also had anemia. HbA1c levels in patients with and without a deprived iron status (absolute or functional) were not significantly different (65 ± 17 vs. 65 ± 16 mmol/mol, p = 0.815). Conclusion: Functional, but not absolute, ID was common in Dutch pediatric DM type 1 patients. HbA1c levels were not associated with ID, which can be explained by the relatively mild deprived iron status in our patients. Trial registration: NTR4642.