Eric Holder pointed out previous home secretaries and judges had indicated Scots-born Mr McKinnon could be extradited to America.
But he denied claims the issue had damaged his relationship with Mrs May, which he said "is and remains strong".
In a victory for Mr McKinnon, pictured, who has been fighting extradition since 2002, the Home Secretary announced last month she would not allow it because he was "seriously ill".
Mr McKinnon, 46, has Asperger's syndrome and suffers from depression. He says he only accessed US government computers to look for evidence of UFOs.
Mr Holder added: "The relationship we have with the UK is a special one."