September in San Juan is the rainiest and the cloudiest month of the year. In September, the weather in San Juan is typically hot. Average daily high temperature in September is about 30 degrees above zero. On average, San Juan has 23 rainy, 4 partly cloudy, and 3 sunny 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 San Juan.