Following the Civil War, both colleges were short on students and on funds, causing them to join together as Washington & Jefferson College.
Before the merger could be completed, Canonsburg residents and Jefferson College partisans filed a lawsuit known as the Pennsylvania College Cases, which sought to overturn the consolidation plan.
On April 4th, Jonathan Edwards, a pastor from Baltimore who had been president of Hanover College, was elected the first president of the unified Washington & Jefferson College.
Canonsburg Academy was reconstituted as Jefferson College, with John McMillan serving as the first President of the Board of Trustees.
Matthew Brown petitioned the Pennsylvania General Assembly to grant Washington Academy a charter, allowing it to be re-christened as Washington College.
The United States Supreme Court upheld the consolidation, allowing the newly configured college to proceed.
Under Brian C. Mitchell, who served as president from 1998 to 2004, the college experienced a growth in construction and an effort to improve relations with the neighboring communities.
Washington & Jefferson College traces its origins to three log cabin colleges established by frontier clergymen John McMillian, Thaddeus Dod, and Joseph Smith.