The comedian has handed over the cash - from a recent libel victory against a U.K. newspaper - to assist Shaker Aamer, the only British resident residing without charge in the camp, take legal action against MI6 chiefs.
Boyle has teamed up with officials of Reprieve, the British-American charity which has long represented inmates, to help Aamer.
Reprieve director Clive Stafford-Smith tells Britain's The Independent newspaper, "If (a newspaper) says something bad about Frankie that embarrasses him or humiliates him then he has the right to sue.
"If, on the other hand, a far more powerful organisation, the British government and their agents, say something about Shaker - whereby instead of being humiliated, he's banged up in prison for 11 years for something he patently didn't do and something he's never been charged with - then the British government's position is Shaker can do nothing."
Aamer was arrested in Afghanistan in 2001 and despite being cleared for release by the U.S. authorities, he has yet to be freed as Americans have insisted on returning him to Saudi Arabia.