The Rogue River National Forest (until 1932 called the Crater National Forest) was established by President Theodore Roosevelt in 1908. The name "Rogue River" commemorates the Takelma tribe, whose defense of their homeland led early day French-Canadian trappers to call them les Coquins, "the Rogues."

The Siskiyou Forest Reserve was established by President Theodore Roosevelt in 1905, and the Reserve was designated as the Siskiyou National Forest in 1907. The name "Siskiyou" is a Cree word for "bob-tailed horse" (bestowed in 1828 by French Canadians working for the Hudson Bay Company).

The Rogue River and Siskiyou National Forests and their nine ranger district offices were administratively combined in 2004. In 2007, the nine ranger districts were consolidated to form five: High Cascades, Siskiyou Mountains, Wild Rivers, Gold Beach, and Powers. Field offices remain in or near the communities of Prospect, Butte Falls, Ruch, Grants Pass, Cave Junction, Gold Beach, and Powers. The Forest also is home of the J. Herbert Stone Nursery, located near Central Point. The Supervisor's Office is located in Medford, Oregon.