Although he personally did not favor secession of Virginia from the Union, at the outset of the American Civil War (1861–1865), he helped form local militia in the Peninsula region of Hampton Roads.

Benjamin Ewell is best remembered for his long tenure as the sixteenth president of the College of William and Mary in Williamsburg before, during and after the American Civil War.

Benjamin Ewell's tireless efforts to restore the historic school and its programs during and after Reconstruction became legendary in Williamsburg and at the college and were ultimately successful, with funding from both the U.S. Congress and the Commonwealth of Virginia.

Enlistments in the Confederate States Army depleted the student body, and on May 10, 1861, the faculty voted to close the college for the duration of the conflict.

[4] In 1861 and 1862, under General John B. Magruder and the Army of the Peninsula, Ewell had the primary responsibility for developing and constructing the Williamsburg Line, a line of defensive fortifications across the Virginia Peninsula east of Williamsburg anchored by College Creek a tributary of the James River on the south and Queen's Creek, a tributary of the York River on the north.

On September 9, 1862, drunken soldiers of the 5th Pennsylvania Cavalry set fire to the college building,[6] purportedly in an attempt to prevent Confederate snipers from using it for cover.

He went to Washington, D.C., and unsuccessfully sought reparations from the U.S. Congress, speaking there several times in an attempt to gain appropriations for the college for the damages done during the War.

It has become legendary at the college and in the Williamsburg community that, every single morning of that long seven-year period, Benjamin Stoddert Ewell would arise and ring the bell calling students to class, so it could never be said that William and Mary had abandoned its mission to educate the young men of Virginia.

[7] In 1888, William & Mary resumed operations under a substitute charter when the Virginia General Assembly passed a bill appropriating $10,000 to support the college as a state teacher-training institution.