January in Flagstaff is the coldest month of the year. In January, the weather in Flagstaff is typically cold. Average daily high temperature in January is about 3 degrees above zero. On average, Flagstaff has 15 partly cloudy, 12 sunny, 3 rainy, and 1 cloudy day in January. The rains are usually light. January as well as February, July, and December is considered the most uncomfortable time to visit Flagstaff.