Junction City is a city in Lane County, Oregon, United States. The population was 4,721 at the 2000 census. In the 1870s, 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, Oregon) re-joined.