Since Pagadian City is a situated within the tropics of the Northern Hemisphere, its climate is characterized by pronounced dry season from January to March, and rainy season from April to December. Rainfall distribution is moderate from 2,500 mm to 3,000 mm annually.

The area is not affected with tropical storms, due to its location which is covered with the mountain ranges of Lanao del Sur on the east-northeast, Cotabato on the east-southeast and Zamboanga del Sur on the north and west.