Flood ranks as the first natural disaster that causes economic losses to human societies. Meanwhile, Iran was reported to be the third country in the world with a high number of affected populations from the flood. In this article, a risk base analysis has been performed to investigate the probable influence of El Niño on the flood damages in Kan River basin (KRB). Doing so, annual precipitation data and Southern Oscillation Index values were gathered for 66 years from 1951 to 2017, then the precipitation change (PC) factor was calculated for every El Niño year. Using a cumulative distribution function of Gumble type fitted on the PC values El Niño changes the precipitation by −10, 8.2, and 31% with 30, 60, and 90% probability levels, respectively. It means that in limited cases El Niño has decreased the flood severity. Also, it could be interpreted that El Niño's influence on the precipitation intensity has been less than +31% by 90% probability and it is less than +8.2% by 60% probability. Considering the PC values with different probabilities, hydrologic and hydraulic models were used to evaluate the runoff, inundation areas, and economic losses to different properties located in the KRB. To have estimates of economic losses as a result of changed precipitation due to El Niño, the damage-depth curves method was used. Flood damage assessment showed that the expected damage cost of a 50-year flood has been reduced as much as −21.77% by a 30% probability. On the other hand, the flood damages may grow up to 40.94 and 73.74%, respectively, by 60 and 90% probability.