Eastern Mennonite Seminary is the outgrowth of the curriculum in Bible at Eastern Mennonite College, and the embodiment of a vision of Mennonite leaders in Virginia, Maryland and Pennsylvania for an institution of higher learning for the training of the denomination’s youth.

In the second decade of the 20th century the vision took concrete form at Harrisonburg after preliminary efforts elsewhere in Virginia. As early as 1918 courses at the college level were offered in advanced biblical training. During the next ten years there was an appreciable increase in college offerings.

By 1937 a four-year Bible program was instituted and within several years it was increased to five years. In the 1948-49 academic year, the Bachelor of Theology curriculum – a two-year post-graduate program – was added. The following years witnessed the continued growth of the program and its gradual development into a division distinct from the college.

In 1960 the curriculum was expanded to encompass three years of study and the Bachelor of Divinity degree was offered for the first time. The Master of Divinity degree was first offered in 1968-69 and the Master of Arts in Religion degree in 1972-73. A one-year program leading to a Certificate in Biblical Studies was first offered in 1974-75. The Master of Arts in Church Ministries emerged as part of a major seminary curriculum revision in 1983-84, and was changed to the Master of Arts in Church (now Christian) Leadership in 1991. A Clinical Pastoral Education Program was added in 1999.

In 1965 Eastern Mennonite Seminary adopted its formal name and an acting dean was appointed. A building funded by seminary donors and designed for seminary programs was dedicated in 1994. Also in 1994, EMS became the graduate theological school of Eastern Mennonite University. In 2019, the seminary joined other EMU programs in the School of Theology, Humanities and the Performing Arts.

In the 1970's, Eastern Mennonite Seminary began offering credit for various pastoral training programs by extension in southeastern Pennsylvania.  In 2008 EMS began offering complete seminary degrees at the EMU Lancaster site.  Today, EMS serves students in all locations by offering courses in on-campus and online formats, so that EMS degrees can be earned from anywhere reliable internet access is available.

Eastern Mennonite Seminary is a graduate division of Eastern Mennonite University. The seminary is an accredited member of the Association of Theological Schools since 1986. It is approved as an institution for the training of candidates for ordination in the United Methodist Church. Eligible students may receive educational benefits from the Veterans Administration.