September in Skagway is the rainiest month of the year. In September, the weather in Skagway is typically cold. Average daily high temperature in September is about 6 degrees above zero. On average, Skagway has 24 rainy, 4 cloudy, and 2 sunny days in September. The rains are usually heavy. September as well as April, May, June, and July is considered the most uncomfortable time to visit Skagway.