The 50-year-old partner at PricewaterhouseCoopers - a former professional soccer player - took the job after US executive Peter Littlewood withdrew from the race to land the top job after failing to win the support of the FA board, despite being the favoured choice of FA chairman Geoff Thomson.
Palios takes over on July 1, replacing Adam Crozier who resigned last year amid a massive row over the commercial exploitation of the FA brands - the England national team and the FA Cup.
Premier League chairman claimed the deals impacted on their own sponsorship arrangements and that their players were being used to promote rival brands.
It created a power struggle which resulted in Crozier deciding to step down.
The FA has also recently been beset by financial problems and recently slashed a fifth of its workforce amid a major series of cutbacks. The new Wembley Stadium scheme is still on track, but the costs have been huge and placed the FA's finances under huge strain.
Said FA chairman Thompson:"We are delighted that Mark has agreed to become the FA's new chief executive.
"First and foremost, Mark's business experience will be a huge asset to us at a time when the FA and the game as a whole must face up to a number of challenges.
"Not only do we remain one of this country's highest profile organisations, but our decision to re-build Wembley means our business and our finances are considerably more complex than at any time in our history.
"Secondly, Mark has played the game at professional level and amateur level and this can only be an asset in his new role as he seeks to build an understanding with players, coaches, managers, fans and fellow football administrators at all levels of the game, both at home and overseas. On behalf of the FA's Board, I wish Mark every success."
Added Palios: "The football industry has changed considerably in recent years. My work at PwC has allowed me to see how the game has developed and provided an insight into some of the challenges I will face.
"From what I can see, the FA has talented and committed staff and loyal high quality commercial partners. The FA enjoys a fabulous name in world football and owns some of the game's most prestigious brands, including, of course, the FA Cup, the England team and Wembley. All of this provides us with a firm foundation on which to take our business forward."
Palios spent 17 years with professional football clubs. He played a total of 400 league and cup games during two spells at Tranmere Rovers and Crewe Alexandra.
Mark Palios has been confirmed as the new chief executive of the English Football Association after months of speculation and rumour.
