Bonner was named for E. L. Bonner, an early settler in Missoula. He was also the first president of the Missoula and Bitterroot Valley Railroad in 1888. Bonner has one of the state's first large sawmills. The first post office was opened in March of 1888 with Lane Paskill as postmaster. A sawmill in Bonner's Ferry, Idaho was also named for this Montana lumber magnate.
Bonner is located in southwestern Montana, just east of Missoula on I-90.