SCC originally opened in 1941 as Fairbury Junior College in Fairbury, Nebraska, suspending operations during World War II and reopening in 1946. Southeast Community College was organized in 1973 with campuses in Fairbury, Lincoln, and Milford. In 1975, Southeast took over the Beatrice campus of John J. Pershing College, which had closed in 1971. In 1980, the agriculture program moved from the Milford campus to Beatrice. In 1986, the original Fairbury location was shuttered and merged into the Beatrice campus. The college includes three campuses and more than 20 off-campus sites in 15 counties.
