As World War II came to a close, Mennonite families in the Ephrata area sought for a better way to educate their children. Although this would be the first Mennonite school in northern Lancaster County, the same goals and philosophy started Lancaster Mennonite High School in 1942. Several Mennonite elementary schools also started in nearby areas between 1939 and 1945.
Ephrata Mennonite School welcomed 83 students in grades 1-9 in September 1946. There were two well-filled classrooms in the first year, with one teacher for grades 1-4 and a teaching principal for grades 5-9. The school board, appointed by several local Mennonite congregations, hired several teachers. Several Mennonite church leaders were asked to advise the board. Although there was a strong tie to the Mennonite congregations in the area, area church leadership gave the school board autonomy to run the school. Tuition, along with additional help from congregational offerings and interested contributors, largely supported the financial needs of the school
Construction of a third classroom finished in 1948. A building program in 1958 added two more classrooms with enrollment reaching 160 by 1965. Building programs in 1977 and 1981 expanded the school to ten classrooms and adequate office space. A two-year building program from 1989-1991 added a gymnasium, library, music room, and kitchen.
In the 1990s, discussion began regarding adding Grades 10-12 to create a K-12 school. It was in 2005-2006 that EMS added a self-paced independent study program for tenth grade. Then in 2008-2009, the school added classroom instruction for Grades 10 and 11. The board hired an additional faculty member to teach high school subjects. The following year, the school began to offer classroom instruction for Grades 10-12, added a part-time faculty member, purchased a modular unit, and renovated to provide two additional classrooms for the budding high school. In May 2010, Ephrata Mennonite celebrated the graduation of the first senior class.