He becomes the managing director of Triple S Communications, part of Paul Stretford's Triple S Sports & Entertainment Group, whose clients include England and Manchester United star Wayne Rooney, various other football players and managers, and sporting events and charities such as Soccer Aid.
The group is also a rights holder for the Premier League, the Championships at Wimbledon and the PGA European Tour, among others.
Formerly an ITV publicist, Whittle joined the FA in 2005 in part to deal with non-sporting media's interest in the delays and problems associated with the construction of the new Wembley Stadium, which eventually opened in 2007. Prior to ITV, he had worked for the BBC.
He was one of the most senior PR staff working with four different England managers during his time at the FA, latterly under comms director Amanda Docherty, who arrived in February this year. His departure follows that of FA head of media operations Joanne Budd, who has taken a job at Crystal Palace Football Club.
Triple S Communications is a newly created agency in the broader Triple S group, which will handle a number of the group's clients, including Rooney, and may also look to expand through acquisition. An undisclosed number of the group's 15 staff will work for the comms agency.
It will be based in London and work in tandem with Red Lantern Digital Media, another agency owned by the group, which has three full-time staff in London, two in Beijing, and a number of part-time consultants..
The group was founded in 2008 by football agent Paul Stretford, and father and son businessmen Freddie and Kenneth Shepherd, who formerly owned Newcastle United. It is headquartered in Cheshire.
Stretford said: "We are delighted to appoint someone of Mark’s calibre to the Triple S team. He will help expand our business across the thriving UK public relations, sport and entertainment industries. Given his pedigree he will bring our clients a level of expertise that very few competitors can provide."
Whittle said Stretford's firm had "led the way utilising the power of social media in football", going on to say: "Wayne Rooney now engages with more than 40 million followers across his personal channels - all thanks to the work of the current in-house digital team and Red Lantern’s international connections."
Rooney himself said: "I’ve worked with Mark for a long time while playing for England and I’m delighted he’s joined the Triple S team."
Ian Monk Media Consultancy, a separate company that handles Rooney's personal PR, retains the footballer as a client.