It was constructed during 1867–68 at the request of Robert E. Lee, who was president of the school (then known as Washington College), and after whom the university is, in part, named.

The centerpiece of the apse of the chapel—in the place where an altar is located in the traditional plan of a Christian church—is a statue of Lee, in his uniform, asleep on an unnamed Civil War battlefield.

The keynote speaker, John W. Daniel, soon to be a U.S. senator from Virginia, and filling in for the absent Jefferson Davis, said of Robert E. Lee's decision to lead the armed forces of Virginia at the outset of the Civil War, "Since the Son of Man stood upon the Mount, and saw 'all the kingdoms of the earth and the glory thereof' stretched before him, and turned away from them to the agony and bloody sweat of Gethsemane, and to the Cross of Calvary beyond, no follower of the meek and lowly Saviour can have undergone more trying ordeal [than Lee].

Daniel lamented that Lee had died a prisoner on parole, his American citizenship never fully restored: "The country which gave the right of suffrage to the alien ere he could speak its language, and to the African freedman ere he could read or understand its laws, denied to him the privilege of a ballot ... himself and his Commander-in-Chief [Davis] constituting the most conspicuous of its political slaves.

Lee's favorite horse, Traveller, is buried just outside the Chapel, where many visitors leave coins, apples, and other tributes.

In the basement of the Chapel is a museum that illuminates the history of the families of George Washington and Robert E. Lee as well as that of the university itself.

First-year students have assembled there to hear the president of the University's student-run Executive Committee speak on the school's Honor System.