The 41-year-old has been officiating in the Barclays Premier League for over a decade but this will be his first time in charge of the Wembley showpiece event.
Clattenburg - who was in charge of Atletico Madrid's Champions League semi-final first-leg victory over Bayern Munich on Wednesday - has previously refereed at Wembley.
He took charge of the 2012 League Cup final and men's Olympic final as well as the 2013 Community Shield - in which Man United beat Wigan 2-0 in David Moyes' first game in charge.
On May 21, the Red Devils will participate in their first FA Cup final since 2007, when they lost the first final at the rebuilt Wembley to Chelsea.
Anthony Martial scored a stoppage-time winner to send Louis van Gaal's side to the final, where they will meet Alan Pardew's Crystal Palace in a repeat of the 1990 event - won by United.
Clattenburg, from County Durham, will be aided by assistant referees John Brooks and Andrew Halliday, while Neil Swarbrick will be the fourth official and Michael Salisbury fills the role of reserve assistant referee.
Clattenburg said it would be an honour to take charge of the final, and recalled the last meeting between the two sides 26 years ago.
"I think every referee who hasn't refereed the Cup final works hard every season to hopefully referee one of the most prestigious and important cup finals in the world," he said.
"You set yourself goals at the start of the season, and mine was to referee in The FA Cup final
It's an honour and a massive achievement.
"It came out of the blue
These days you get told of what games you're doing by text, but when you see a call coming in from The FA referees' department you know it's important.
"I remember watching Manchester United and Crystal Palace and the tradition of these two teams 26 years ago and that famous game - it's amazing how these games relive.
"Hopefully it will be as good as it was all those years ago."
Clattenburg has officiated 27 Premier League games so far this season, showing 81 yellow cards and six reds.
He will next take charge of Chelsea v Tottenham on Monday night, a match which could yet decide the destiny of this season's title.
It was during the officiating of a Chelsea v Man United match in 2012 in which Clattenburg was accused of using racial language at Blues midfielder John Obi Mikel.
After being cleared by the Football Association and having a police investigation dropped, Clattenburg returned to top-level officiating having said the thought of his career coming to an end had been 'truly frightening'.
Source : PA
Source: PA