He was the second son of a career U.S. Army officer, ultimately Colonel Thomas Turner Fauntleroy and his wife, the former Ann Magdalene Magill.

Thomas Jr. received a private education suitable for his class, including at Benjamin Hallowell High School in Alexandria and the University of Virginia in Charlottesville, where he studied law and graduated in 1844.

[3] As the American Civil War began, the elder Fauntleroy gave up his U.S. Army commission and returned to Virginia, where he lived with this son.

His eldest son C. M. Fauntleroy also resigned his U.S. Navy commission, but the ship he commanded, the CSS Rappahannock, was never permitted to leave European waters.

Despite health problems following the Civil War, after agreeing not to again own enslaved people and receiving a presidential pardon on September 29, 1865,[4] Fauntleroy resumed his legal practice and political career.