September in El Nido is the cloudiest month of the year. In September, the weather in El Nido is typically hot. Average daily high temperature in September is about 28 degrees above zero. On average, El Nido has 26 rainy, 2 cloudy, and 2 partly cloudy days in September. The rains are usually heavy. September as well as May, June, July, and August is considered the most uncomfortable time to visit El Nido.