In September, the weather in Kota Kinabalu is typically hot. Average daily high temperature in September is about 29 degrees above zero. On average, Kota Kinabalu has 21 rainy, 5 cloudy, 3 partly cloudy, and 1 sunny day in September. The rains are usually heavy. September as well as January, March, April, and May is considered the most uncomfortable time to visit Kota Kinabalu.