Soybean cyst nematode (SCN), Heterodera glycines, HG type 1.2.5.7 is the most virulent and widespread SCN biotype in the southern states of the USA, but its effect on soybean (Glycine max [L.] Merr.) nitrogen fixation (NF) activity and growth is not well documented. The objectives of this study were to: (1) measure the impact of HG type 1.2.5.7 on NF activity during the early vegetative stage of three soybean genotypes and (2) compare the impact on soybean leaf and root development, and plant growth. The NF activity of two susceptible (S) genotypes ("Ellis" and "Williams 82") and one resistant (R) genotype (PI 88,788), subjected to a 10,000-egg treatment, was measured using an in-situ flow-through acetylene reduction assay. The average NF activity of the soybean genotypes was decreased by SCN activity. Time points assessment showed that the NF activity was differently impacted among the genotypes. Based on the measured values, the NF activity was decreased by 30% in SCN infected plants of Williams 82 but that of PI 88,788 and Ellis was affected. Likewise, soybean leaf color and leaf area were affected by SCN infection, but there was no impact on root length and root area. These results showed that SCN HG type 1.2.5.7 can exhibit varying negative impact on NF and shoot growth of S soybean genotypes, while R genotypes may be unaffected. Thus, indicating genetic resistance continues to be a critical tool for the management of the SCN.