Soil waterlogging limits plant growth and has a major impact on agricultural productivity. Here, we tested the hypothesis that the overexpression of the NCED gene improves waterlogging and reoxygenation tolerance in soybean plants. This was tested using a transgenic soybean line overexpressing the NCED gene (2Ha11) and the conventional cultivar BRS184 (wild-type; WT), which is the genetic background of the 2Ha11 line. Plants at vegetative (V6) and reproductive (R2) stages were exposed to waterlogging for 60 h and posterior reoxygenation for an additional 60 h. Overall, the NCED overexpression increased the levels of lipid peroxidation in plants exposed to waterlogging and posterior reoxygenation while decreased the antioxidant activity and alcohol dehydrogenase activity. In addition, NCED overexpression decreased seed weight and grain yield in the 2Ha11 line exposed to waterlogging at the reproductive stage. Taken together, these results suggest that the overexpression of NCED triggers an increased waterlogging sensitivity in soybean plants especially when they are exposed to waterlogging at the reproductive stage.