Lincoln College was established as Lincoln University in 1865 by the Cumberland Presbyterian Church and was named after Abraham Lincoln. There were a few sites that were looked at as possibilities for the institution, before Lincoln, Illinois; however, in December 1864, the City of Lincoln was chosen.
On February 6, 1865, the Illinois General Assembly granted the charter that established the university. The groundbreaking for University Hall, the first college building, was held on Abraham Lincoln's last living birthday, six days after the charter had been granted; in September 1865 the building's foundation was completed, and the cornerstone was laid. In November 1866, the college opened its doors to men and women alike. In 1868, three people had earned their degrees.
In 1901, Lincoln College affiliated with the Decatur College and Industrial School (now Millikin University) in Decatur. The name of the school was changed from Lincoln University to Lincoln College of the James Millikin University. James Millikin, a wealthy Decatur livestock breeder, offered Lincoln University a $50,000 grant for a new building at the Lincoln campus if the school would turn over its charter. The $50,000 grant was on the condition that the citizens of Lincoln would raise $25,000 towards the new building project. The $25,000 was raised, and the $50,000 grant was provided to the Lincoln campus.
In 1929, Lincoln became a two-year junior college, no longer offering four-year degrees as it had done since its inception. Many junior colleges were created in the 1920s and 1930s. The move helped the college through the financial problems of the Great Depression and World War II.
The Lincoln College campus experienced substantial growth following World War II. The college had seven dorms, numerous classroom buildings, a library, and a new building dubbed the Lincoln Center, which hosted a gymnasium, state-of-the-art classrooms, and Lincoln Heritage Museum.
In 1974, Lincoln College received a license for radio station WLNX.
Since 2010, Lincoln has been recognized as a Predominantly Black Institution (PBI) by the U.S. Department of Education.
In 2015, David Gerlach was selected as the 22nd President of College. Shortly after Gerlach's appointment, the Lincoln College Board of Trustees approved a plan to return Lincoln College to its roots as a full bachelor's degree-granting institution while retaining its associate degree programs.