Waterlogging is a common form of abiotic stress that severely impedes global soybean production. Targeting this issue, an experiment was carried out at Sher-e-Bangla Agricultural University during August–November 2019 to screen out the waterlogging tolerance and yield performances of selected soybean genotypes. The experiment was laid out in a completely randomized design (CRD) with three replications consisting of 2 water levels (control and waterlogging) and 12 genotypes (Sohag, BARI Soybean-5, BINAsoybean-1, BINAsoybean-2, BINAsoybean-3, BINAsoybean-5, BINAsoybean-6, SGB-1, SGB-3, SGB-4, SGB-5, and GC-840). On the 15th day after sowing, plants were exposed to waterlogging for 12 days. Waterlogging remarkably declined the growth and yield of all the soybean genotypes compared to control. Reduced plant height, relative water content, above-ground fresh and dry weight, SPAD value, leaf area, number of leaves, branches, pods, seeds pod−1, 100-seed weight, and seed yield plant−1 were observed under waterlogging stress. Conversely, mortality rate and electrolyte leakage were increased under the same condition. The waterlogged plants showed delayed flowering and maturity compared with the control plants. However, among the 12 genotypes, Sohag, BARI Soybean-5, GC-840, BINAsoybean-1, and BINAsoybean-2 showed better waterlogging tolerance. These genotypes showed a greater number of adventitious roots in the base of their stem, which probably helped plants to thrive under waterlogging conditions.