The Blue Mountains constitute one of the largest uplifts in Oregon and the main range, together with its spurs and offshoots, extends into several counties. The Blue Mountains are separated from the Wallowa Mountains by the Powder River and Grande Ronde River.

The highest point in the Blue Mountains is Rock Creek Butte, a peak on Elkhorn Ridge a few miles west of Baker City with an elevation of 9097 feet. Strawberry Mountain near Prairie City is almost as high, with an elevation of 9052 feet.