Efficient operation of rainwater pumping stations is essential for mitigating urban flooding under climate change. This study focuses on the Samcheok Osipcheon watershed, located in Gangwon-do, South Korea, and proposes a deep learning-based inflow prediction framework for the Samcheok-si drainage system using SWMM-simulated datasets. A total of 900 rainfall scenarios were generated and used to train three models: ANN, CNN, and LSTM. All models reproduced inflow hydrographs with high accuracy, but the CNN model showed overfitting with oscillations in the recession limb. The LSTM model demonstrated the best performance, achieving an NSE of 0.97 and a PPE of 3.45%. Based on the predicted inflow, two pump operation strategies were evaluated. The proactive operation considering upstream surcharge conditions, combined with second-level control, reduced peak water levels from 2.585 m to 2.439 m (approximately 5.6%) compared to the conventional operation. In addition, second-level pump operation reduced excessive discharge and stabilized detention basin water levels. The results indicate that the proposed framework can support real-time pump operation, enhance the resilience and sustainability of urban drainage systems, and contribute to sustainable urban flood mitigation.