Junction City was named by railroad magnate Ben Holladay, who decided this would be where the rail line on the east side of the Willamette Valley would meet the rail line on the west side. The westside line, however, was not built according to plan, although Junction City later was where the two main branches of U.S. Route 99 (which divided in Portland) would rejoin. The city was incorporated in 1872.
Junction City gained media attention from major outlets such as CNN, Fox News, and The Today Show in 2003, when a number of local men posed in the nude for "The Men of the Long Tom Grange Calendar" to raise money for the local school district. The project raised over $265,000 for local schools and brought national attention to the issue of school funding.