The development of soybeans tolerant to the soybean aphid [Aphis glycines Matsumura (Hemiptera: Aphididae)] remains unexplored. The objectives of this research were to determine the susceptibility of two high-yielding soybean [Glycine max (L.) Merrill (Fabales: Fabaceae)] genotypes involved in a breeding platform to develop aphid-tolerant recombinant inbred lines (RILs); characterize the peroxidase activity and relative expression of peroxidase transcripts in the parents of RILs; and identify an assay to phenotype aphid-tolerant RILs. Enzyme kinetic assays documented the total peroxidase activity for tolerant (KS4202), susceptible (SD76R), and two high-yielding (U09105007 and U11-611112) soybeans during two vegetative stages (V1 and V3) at three sampling days (D4, D6, and D8 after aphid introduction). Enzyme kinetic assays showed that V3 infested tolerant and U11-611112 plants had significantly higher peroxidase activity than their respective control plants at D4, and infested tolerant plants were also higher than control plants at D6.There were no apparent trends when comparing the expression of peroxidase-specific transcripts in the absence of aphids (basal levels) in both V1 and V3. Relative expression analyses of two peroxidase transcripts (PRX52 and PRX2) performed to compare differences among the soybean genotypes indicated that, despite basal levels being similar for the treatments analyzed, tolerant soybeans had a tendency for a higher expression of PRX52 in the presence of aphids. Based on the different patterns observed and the feasibility of analyses performed in this study, enzyme kinetics using V3 infested plants may be a marker for screening RILs in a breeding program targeting the development of aphid-tolerant soybeans.