Urban flooding has become increasingly frequent due to the rising intensity of rainfall driven by urban development and climate change. Effective prevention measures are crucial to mitigate the significant human and material damages caused by such events. Rapid and accurate pre-detection techniques can help to reduce the impacts of urban flooding. With the advancement of deep learning, deep neural networks (DNNs) have been successfully applied across various domains, including computer vision and speech recognition. In particular, DNNs for computer vision demonstrate high performance with relatively low computational costs. In this paper, we propose a flooding region segmentation model for urban underpasses based on the U-Net architecture. To train and evaluate the model, we collected datasets from the Mannyeon, Oryang, and Daedong underpasses in Daejeon. The proposed method achieved Dice coefficients of 98.8%, 94.03%, and 93.85%, respectively. This model demonstrates high segmentation performance in detecting flooded regions and can be integrated into continuous flood monitoring systems.