Chiyoda basin is located in Saga Prefecture in Kyushu Island, Japan, and lies next to the tidal compartment of the Chikugo River to which the excess water in the basin is drained away. Chiyoda basin has a total area of about 1,100 ha and is a typical flat and low-lying paddy-cultivated area. The main problem in this basin is the appropriate operation of drainage structures during and after flood events in order to minimize the inundation damages for crop yield and to fulfill the irrigation requirement in the irrigation period. This paper presents a mathematical model of a drainage system in Chiyoda basin for calculating the flood inundation and optimizing the operation of gates in a main drainage canal. First, the algorithm of gate operation was simulated and the drainage model was then evaluated by comparing the simulated water levels with those observed during an actual rainfall event. The results show that the observed and simulated water levels are in good agreement, indicating that the proposed model is applicable for drainage and inundation analyses in flat, low-lying paddycultivated areas. Second, the optimization of gate operation was investigated by trial and error method using a stochastic rainfall time series with a return period of 30 years and the tidal conditions of spring and neap tides in the Chikugo River. Comparing a total inundation time, a total inundation area and maximum inundation depth in the paddy tanks at the upstream and the downstream ends, it was concluded that the present operation based on the gate operators' experience was almost the optimal one, and the sooner start of opening operation and the later start of closing operation within the operationality of check gates were recommended to minimize the inundation damage. The present operation could be able to minimize the total inundation time, the total inundation area and the maximum inundation depths in paddy tanks and to meet fully both the drainage and the irrigation requirements.