The war had utterly devastated the South and posed serious questions of how the South would be re-integrated to the Union. The war destroyed much of the wealth that had existed in the South. All accumulated investment in Confederate bonds was forfeited; most banks and railroads were bankrupt. The income per person in the South dropped to less than 40 percent of that of the North, a condition that lasted until well into the 20th century. Southern influence in the federal government, previously considerable, was greatly diminished until the latter half of the 20th century.

Reconstruction began during the war, with the Emancipation Proclamation of January 1, 1863, and it continued until 1877. It comprised multiple complex methods to resolve the outstanding issues of the war's aftermath, the most important of which were the three "Reconstruction Amendments" to the Constitution: the 13th outlawing slavery (1865), the 14th guaranteeing citizenship to slaves (1868) and the 15th ensuring voting rights to slaves (1870).

Numerous technological innovations during the Civil War had a great impact on 19th-century science. The Civil War was one of the earliest examples of an "industrial war", in which technological might is used to achieve military supremacy in a war. New inventions, such as the train and telegraph, delivered soldiers, supplies and messages at a time when horses were considered to be the fastest way to travel. It was also in this war that aerial warfare, in the form of reconnaissance balloons, was first used. It saw the first action involving steam-powered ironclad warships in naval warfare history. Repeating firearms such as the Henry rifle, Spencer rifle, Colt revolving rifle, Triplett & Scott carbine and others, first appeared during the Civil War; they were a revolutionary invention that would soon replace muzzle-loading and single-shot firearms in warfare. The war also saw the first appearances of rapid-firing weapons and machine guns such as the Agar gun and the Gatling gun.