The two-and-a-half year deal also sees the betting firm become sponsor of the England national side through to the next World Cup in 2014.
It will use FA Cup branding to push its online services and is likely to use images of England players in future campaigns.
Kristof Fahy, chief marketing officer for William Hill, says the deal provides “some very good opportunities to develop our brand across a wide variety of channels”.
News of the sponsorship comes as marketing activity around English football’s top club competition increases as Premier League clubs prepare to enter the fray.
Title sponsor Budweiser is running a radio campaign through the third, fourth and fifth rounds featuring Sam Allardyce and Ian Holloway, managers of West Ham and Blackpool respectively.
Both are heard offering pre-match pep talks. Ads conclude with a terrace style chant of “grab some Buds”.
Meanwhile, Manchester City has launched a Twitter competition asking fans to tweet their “inspirational” team talks to captain Vincent Kompany ahead of their third round clash with Manchester United.
The Tweet deemed the most inspirational will receive Kompany’s match day shirt and captain’s armband from the game as well as a signed poster of their motivational speech.