The runoff from heavy rainfall reaches urban streams quickly, causing them to rise rapidly. It is therefore of great importance to provide sufficient lead time for evacuation planning and decision making. An efficient flood forecasting and warning method is crucial for ensuring adequate lead time. With this objective, this paper proposes an analysis method for a flood forecasting and warning system, and establishes the criteria for issuing urban-stream flash flood warnings based on the amount of rainfall to allow sufficient lead time. The proposed methodology is a nonstructural approach to flood prediction and risk reduction. It considers water level fluctuations during a rainfall event and estimates the upstream (alert point) and downstream (confluence) water levels for water level analysis based on the rainfall intensity and duration. We also investigate the rainfall/runoff and flow rate/water level relationships using the Hydrologic Engineering Center’s Hydrologic Modeling System (HEC-HMS) and the HEC’s River Analysis System (HEC-RAS) models, respectively, and estimate the rainfall threshold for issuing flash flood warnings depending on the backwater state based on actual watershed conditions. We present a methodology for issuing flash flood warnings at a critical point by considering the effects of fluctuations in various backwater conditions in real time, which will provide practical support for decision making by disaster protection workers. The results are compared with real-time water level observations of the Dorim Stream. Finally, we verify the validity of the flash flood warning criteria by comparing the predicted values with the observed values and performing validity analysis.