The 40-year-old Scot will give more than £54,000 to Reprieve after securing the sum at the high court where a jury decided he was defamed by the Daily Mirror in an article describing him as "racist comedian Frankie Boyle".
Boyle posted a message on Twitter saying: "Here's the good people I'm giving my damages to. They do a lot of inspiring work. Have a look if you get a minute. reprieve.org.uk."
Reprieve provides legal support to prisoners who are unable to pay for it themselves, the charity's website says.
The website says Reprieve prioritises the cases of prisoners accused of the most extreme crimes as they are "most likely to have their human rights jettisoned or eroded".
Jurors ruled in Boyle's favour after a week-long trial in London. The comic said he had sued because he had always "made a point" of being "anti-racist".
He gave a V-for-victory sign as he left court and said he was "very happy" with the decision.