The eldest son and the second of seven children, Custis Lee, as his family called him, followed his father's footsteps to West Point. At age 16, Custis had been denied entry into the military academy, but his father wrote an appeal to General Winfield Scott and so he was admitted the following year. Though he had needed his father's influence to gain admission, once in West Point Lee made the most of his opportunity. He graduated first in his class of 46 in 1854. For the last two years of his studies, his father was superintendent of the academy.
Lee served in the Engineering Corps until 1860, primarily in California. When Fort Sumter, South Carolina, fell in April 1861, he was stationed in Washington, D.C. Lee resigned his commission on May 2, 1861, about two weeks after his father resigned from the U.S. Army, and became a captain in the Confederate Army, assisting in the construction of fortifications for Richmond, Virginia.
In August 1861, Confederate President Jefferson Davis selected Lee to serve as his aide-de-camp, and he was soon promoted to colonel. Custis Lee spent the next three years in this position, gathering military information for Davis and conferring with him on a wide variety of military issues. For his service, he was promoted to brigadier general in 1863.
During the Gettysburg campaign, when his father's army was in Pennsylvania, Lee commanded part of the force defending Richmond, and he oversaw the Richmond defenses during Union General Ulysses S. Grant's Virginia campaign of 1864. He also assumed leadership of a division in October 1864, but his command saw action only when the Confederates evacuated Richmond in March 1865. He and his force were captured at Sayler's Creek, Virginia, a few days before his father surrendered the rest of the Army of Northern Virginia on April 9, 1865.
After the war, Custis Lee taught engineering at the Virginia Military Institute. In 1871, he replaced his late father as president of Washington College (later renamed Washington and Lee University). Custis Lee retired from that post in 1897, and died in Fairfax County, Virginia, on February 18, 1913.