Even while the Civil War was in progress, the federal government offered amnesty to Confederate citizens in an attempt to encourage loyalty to the Union and to begin the process of reconstruction. The Confiscation Act of 1862 authorized the president of the United States to pardon anyone involved in the rebellion. The Amnesty Proclamation of December 8, 1863, offered pardons to those who had not held a Confederate civil office, had not mistreated Union prisoners, and would sign an oath of allegiance. Another limited amnesty that targeted Southern civilians came into effect on May 26, 1864.

On April 9th 1865, when General Robert E. Lee surrendered his Army of Northern Virginia to General Ulysses S. Grant, the men and officers were allowed to return to their homes, not to be disturbed by United States authority so long as they observe their paroles and the laws in force where they may reside. This stipulation allowed Confederate soldiers to return to their homes without the threat of trials for treason.

On May 29, 1865, President Andrew Johnson provided for amnesty and the return of property to those who would take an oath of allegiance. However, former Confederate government officials, officers with the rank of colonel and above from the Confederate army or lieutenant and above from the Confederate navy, and people owning more than $20,000 worth of property had to apply for individual pardons. Though it was difficult for ex-Confederates to ask for a pardon for something they did not believe had been wrong, thousands did ask for and receive amnesty from President Johnson.

On Christmas Day 1868, Johnson granted an unconditional pardon to all Civil War participants except high-ranking military and civil officials. In May 1872 the Congressional Amnesty Act gave the right to hold office again to almost all Southern leaders who had been excluded from public office by the 14th Amendment.