In 2003 Nick Newlife, from Oxfordshire, made a wager of £1,520, at odds of 66/1, that the Swiss tennis star would win seven Wimbledon titles by 2019.
Mr Newlife died in 2009 but had left the betting slip to Oxfam in his will.
Federer's defeat of Britain's Andy Murray in Sunday's Wimbledon final means the charity will now collect a payout from William Hill of £101,840.
Andrew Barton, from Oxfam, told  
          5 live
's  
          Stephen Nolan
 that it had been a difficult match to watch because his loyalties were split.
"It's just so unfortunate that he nailed it against Andy Murray," he said.
"I was just sitting there watching the tennis and I kept finding myself calling for Murray, particularly in that long game in the third set.
"And then my head is telling me: Andrew, remember Oxfam gets the money if Federer wins."
Mr Newlife, from Tackley, who was 59 when he died, had written to William Hill requesting the bet in 2003.
Spokesman for the bookmaker Graham Sharpe has described the wager as "unique".
William Hill said it had already paid out £16,750 to Oxfam from another bet placed by Mr Newlife, of £250 at 66/1, that Federer would win 14 Grand Slam events.
The Swiss reached that mark at the 2009 French Open and is now a 17-time Grand Slam champion.
A bet placed on Wimbledon champion Roger Federer nearly a decade ago has netted more than £100,000 for Oxfam.