Source: http://www.archives.gov/publications/prologue/2005/spring/piece-lee.html
"On October 2, 1865, the same day that Lee was inaugurated as president of Washington College in Lexington, Virginia, he signed his Amnesty Oath, thereby complying fully with the provision of Johnson's proclamation. But Lee was not pardoned, nor was his citizenship restored. And the fact that he had submitted an amnesty oath at all was soon lost to history.
More than a hundred years later, in 1970, an archivist at the National Archives discovered Lee's Amnesty Oath among State Department records (reported in Prologue, Winter 1970). Apparently Secretary of State William H. Seward had given Lee's application to a friend as a souvenir, and the State Department had pigeonholed the oath.
In 1975, Lee's full rights of citizenship were posthumously restored by a joint congressional resolution effective June 13, 1865.
At the August 5, 1975, signing ceremony, President Gerald R. Ford acknowledged the discovery of Lee's Oath of Allegiance in the National Archives and remarked: "e;General Lee's character has been an example to succeeding generations, making the restoration of his citizenship an event in which every American can take pride."