[2] The county is named after Mount Jefferson, the second tallest mountain in Oregon.

The county owes much of its agricultural prosperity to the railroad, which links Madras with the Columbia River, and was completed in 1911, and to the development of irrigation projects in the late 1930s.

The railroad was completed despite constant feuds and battles between two lines working on opposite sides of the Deschutes River.

The first (temporary) county seat was Culver, which was selected by a three-man commission appointed by the governor.

The deadlock was eventually broken by allowing the Metolius Commissioner to post the tie-breaker, by voting for Culver.

[citation needed] Rapid development in adjacent Deschutes County during the 1990s had farmers in Jefferson County concerned that they might be priced out of their own farmlands, which could be replaced by destination resorts, golf courses and other amenities for recent arrivals.

Though Jefferson County is located in central Oregon, politically it falls in line with the eastern side of the state.

[17] Agriculture is the predominant source of income in the county, with vegetable, grass and flower seeds, garlic, mint and sugar beets cultivated on some 60,000 acres (240 km2) of irrigated land.

Jefferson County also has vast rangelands and until 2016 had an industrial base related to forest products.

The Warm Springs Forest Products Industry, a multimillion-dollar complex owned by the Confederated Tribes of Warm Springs — partially located in the northwestern corner of the county — was the single biggest industry.