Kraybill Mennonite School opened its doors on September 6, 1949, in what is now known as the Meetinghouse. It was part of Lancaster Mennonite School.

In 1971, Kraybill Mennonite School separated from Lancaster Mennonite School and was governed by its own board.

In 2006, Kraybill Mennonite School merged with Lancaster Mennonite School (later referred to as LM).

On March 13, 2018, LM Administration sent notice that it was planning to close the Kraybill campus.

On March 25, 2018, after strong Kraybill community support and a persuasive case put forth by the Kraybill Site Council, the LM Board of Directors voted to not close the Kraybill campus and to instead pursue an affiliate relationship with Kraybill.

On November 9, 2018, Lancaster Mennonite and Kraybill Mennonite School signed an agreement for Kraybill to become a separate independent school on July 1, 2019, as it existed from 1971 to 2006.

The final deed transfer back to Kraybill Mennonite School was recorded in Lancaster County on 12/12/19.