Iron deficiency anemia (IDA) is common in infants and the fortification of infant formula with iron is an effective preventive strategy. Because of the severity of cow's milk allergy and the popularity of vegetarianism, soy-based infant formula has been widely used. However, whether soy-based infant formula is detrimental to iron absorption and increases the risk of IDA in infants requires further investigation. In this study, FeSO4 and its potential alternative encapsulated ferric pyrophosphate (FePP) were dissolved in soy protein and whey protein solution, and administered to IDA suckling rats by gavage to investigate the effects of protein system on the IDA remission by iron. Results showed that both types of iron supplement increased the body weight and improved the organ coefficients of IDA suckling rats irrespective of the protein system. In addition, for each type of iron supplement, both protein systems had the same recovery effects on hemoglobin, red blood cell count, hematocrit and body iron status. And, soy protein did not affect the expression of key iron absorption proteins or genes in the suckling rats. In conclusion, for IDA suckling rats, either FePP or FeSO4 in soy protein system has the same beneficial effect as whey protein system, and can effectively improve IDA. These findings provide a reference for the further application of soy-based infant formula and novel iron supplements.