The school is named for a biblical location found in Exodus 15:27, wherein Elim is described as an oasis in the wilderness.

[7] The Elim campus in Lima was originally the site of Genesee Wesleyan Seminary of the Methodist Episcopal Church, which opened in 1831 as one of the first coeducational schools in the United States, constructing the buildings now known as College Hall and Spencer Hall in the Greek Revival style.

[9] The Methodist Church operated a new Genesee Junior College at the site from 1947 to 1951, when Elim Bible Institute bought the 75-acre (300,000 m2) campus and buildings for $75,000.

The incorporated Fellowship continues to support Pentecostal and Charismatic churches, ministers, and missions, providing credentials and counsel for ministers, encouraging fellowship among local churches, sponsoring leadership seminars, and also serving as a transdenominational agency sending missionaries and other personnel to other countries.

[21] Randall Terry (class of 1981) and Rob Schenck founded the anti-abortion activist group Operation Rescue after studying together at Elim in the early 1980s.