Background Cell surface transferrin receptor 1 (TFR1) is a gatekeeper controling cellular iron uptake. The association of iron-deficiency anemia (IDA) in humans with TFR1 variants was not extensively studied. Among these variants is TFR1 rs3817672, an exonic missense variation that may affect the TFR1 protein structure. This is the first study in Egypt and the second worldwide that genotype TFR1 rs3817672 variant in IDA pediatric patients. Aim The aim of the current study was to investigate the association between TFR1 rs3817672 variant with susceptibility risk for IDA. Patients and methods The study was conducted on 50 IDA Egyptian pediatric patients and 50 healthy controls. Complete blood count, iron profile, and TFR1 rs3817672 variant genotyping were performed for all participants. Results TT genotype was associated with a high risk of IDA among cases compared to controls in the recessive model (odds ratio 24, 95% confidence interval 5.253–109.650, P≤0.001) with the predominance of T allele (odds ratio 7.3187, 95% confidence interval 3.919–13.669, P≤0.001). TT genotype was associated with a significant decrease in serum iron (P=0.001 and 0.003) and transferrin saturation (P=0.003 and 0.005) compared to CT genotype and CC+CT genotypes in the recessive model, respectively. In IDA patients, serum iron had a significant positive correlation with transferrin saturation (r=0.984, P≤0.001) and a significant negative correlation with total iron-binding capacity (r=−0.555, P≤0.001). Conclusion TT genotype was the predominant genotype among Egyptian pediatric IDA patients. TFR1 rs3817672 genotyping might be used as a potential screening test for IDA risk susceptibility in pediatrics.