NAC transcription factors play important roles in plant growth, development and stress response. Previously, we identified multiple NAC genes in soybean. Here, we identify the roles of two genes, GmNAC11 and GmNAC20, in stress response and other processes. The two genes were differentially induced by multiple abiotic stresses and plant hormones, and their transcripts were abundant in roots and cotyledons. Both genes encoded proteins that localized to the nucleus and bound to the core DNA sequence CGT[G/A]. In the protoplast assay system, GmNAC11 acts as a transcriptional activator, whereas GmNAC20 functions as a mild repressor; however, the C-terminal end of GmANC20 has transcriptional activation activity. The overexpression of GmNAC20 enhances salt and freezing tolerances in transgenic Arabidopsis plants; however, GmNAC11 overexpression only improves salt tolerance. The overexpression of GmNAC20 also promotes lateral root formation. GmNAC20 may regulate stress tolerance through the activation of the DREB/CBF-COR pathway, and it may control lateral root development by altering auxin signaling-related genes. GmNAC11 likely regulates DREB1A and other stress-related genes. The roles of the two GmNAC genes in stress tolerance were further analyzed in soybean transgenic hairy roots. These results provide a basis for genetic manipulation to improve the agronomic traits of important crops.