Iron deficiency anemia (IDA), which causes greater morbidity and mortality in children, has multifactorial causes, including many helminthic and protozoal infections. Herein, the study aimed to find out the frequency and associated risk of Blastocystis sp. infection among children with IDA, together with the estimation of the serum levels of iron, zinc, copper, and vitamin A. Both stool and blood samples were obtained from 90 children with a confirmed diagnosis of IDA and 90 non-anemic children. Blastocystis sp. was diagnosed by direct stool examination and Invitro cultivation methods. Different hematological parameters were recorded, and the serum level of iron, zinc, copper, and vitamin A was measured in serum samples. The overall predominance of Blastocystis in children was 36.7%, significantly higher (P < 0.001) in children with IDA (55.6%) compared to non-anemic controls (17.8%). Furthermore, Blastocystis infected children were 5.781 times more prone to be anemic (OR = 5.781). All IDA cases with positive Blastocystis infection had a mean hemoglobin level of 9.55 g/dl (moderate anemia). While in other non-infected IDA cases, it was 9.56 g/dl, showing no statistical difference (P = 0.845). Serum levels of zinc, iron, and vitamin A considerably decreased, whereas serum copper levels significantly increased in IDA children infected with Blastocystis. The current research is the first in Egypt to indicate that Blastocystis infection in children is a high-risk factor for developing IDA. Blastocystis infection significantly alters the metabolic and biochemical processes and interferes with the absorption of micronutrients and vitamin A in IDA children.