The betting firm has replaced Betfred as the official betting partner of the Premier League champions.
As part of the deal, Betfair will use the Manchester United logo in marketing activity. and run perimeter board signage.
The gambling firm has also launched football website www.betfairfootball.com , which will include content from Manchester United players.
To mark the three-year deal, the gaming company has introduced the “Betfair Goal Challenge”, which will see United strikers Wayne Rooney, Michael Owen and Dimitar Berbatov compete to score the most goals over the coming season.
Each League strike will earn £1,000 for the Manchester United Foundation.
The partnership is the first Betfair has agreed with a football club since its one-year shirt deal with Fulham in 2003 and has to now concentrated its efforts on cricket and horse racing.
It is the official betting partner of the England & Wales Cricket Board and at all test match grounds.
The firm joins rivals including 188BET and Paddy Power in signing official partnership agreements with clubs.