A native of Vermont, Babcock graduated third in his class at West Point in 1861, and served in the United States Army Corps of Engineers throughout the Civil War. As Assistant Engineer and aide-de-camp for district commander Nathaniel P. Banks, in 1862 Babcock worked on fortifications to aid in defending the nation's capitol from Confederate attack. Babcock later served as aide-de-camp for Ulysses S. Grant and participated in the Overland Campaign. He was promoted to brevet brigadier general in 1865 and continued on Grant's staff during Reconstruction. In 1867, Babcock warned Grant of a white supremacist insurgency that used Confederate symbolism to intimidate blacks in the South.