The history of Evangelical Bible Institute begins in February of 1994. The first initiative, led by Lithuania Christian Fund and implemented at Klaipeda Baptist Church, was known as “Congregational Leadership Development Program.”

In January 14, 1997, the program was transferred to the new facilities of Lithuania Christian Fund in  Siauliai . With the renaming of the program into  “Evangelical Bible Institute“ – its contents changed as well. Its focus shifted to equipping potential church leaders with the foundations of theological education.

In 2000 several pilot seminars were organized in order to estimate the needs for theological education in local communities. The same year a primary congregational analysis was conducted. Its results served as the basis for the completion of 6 month long strategic planning process. The assessment of the previous EBI activity showed that the new program needs to be adjusted to meet the needs of a wider circle of Christians. Consequently, the program was reorganized as a semi-distance Foundational Theological Training  program, with 13 new students joining it in September, 2001.

In 2005, the school reorganized its program into two distinct programs: the Bachelor of Christian Ministry and the Bachelor of Pastoral Ministry. In 2006, both of these programas were granted the status of “Candidate for Accreditation” by Euro-Asian Accrediting Association (EAAA).

In 2012, the school was registered as an independent academic institution with a status of public enterprise. Its newly formed board of trustees came to consist of the representatives of seven Christian organizations and denominations.

In the Fall of the same year, a new center for EBI studies, in Vilnius, was opened. Simultaneously, at the advice of the board of trustees, the school began a new, Bachelor of Theology (6-year), program.

In April of 2015, all three of EBI's programs were granted full accreditation by the Euro-Asian Accrediting Association.