September in Cape Girardeau is the sunniest month of the year. In September, the weather in Cape Girardeau is typically warm. Average daily high temperature in September is about 27 degrees above zero. On average, Cape Girardeau has 16 sunny, 7 rainy, 5 partly cloudy, and 2 cloudy days in September. The rains are usually heavy. September as well as October is considered the most comfortable time to visit Cape Girardeau.