The 25-year-old spent last season on loan at Aston Villa from Manchester United and Villa had been keen to secure the midfielder’s services on a permanent basis.
Everton, however, have agreed a five-year contract with Cleverley and he will officially join on 1 July once his United contract has expired.
Roberto Martínez has pursued the midfielder since last summer, when United refused to sanction his season-long loan to Goodison. The pair worked together at Wigan Athletic in the 2010-11 season when Cleverley scored four goals in 25 appearances while on loan with the Latics.
Martinez: “We are extremely delighted to be welcoming Tom to Everton and I can think of many reasons as to why our fans will enjoy Tom representing our football club.
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“The most important one is that he is a perfect fit for what we are trying to build here as he has so much experience of playing in the Premier League and he still has his best years just ahead of him.
“At the age of 25 and a player who is representing his country, Tom has experienced winning trophies and having big roles in demanding teams. Having worked with him previously, I know the type of character he is and I know that, with the Everton fans’ support, we will get a very special footballer joining our already exciting team.
“It says a lot also, when someone like Tom is available on a free transfer and he can pick his next club out of many options home and abroad, that he has chosen to play for our football club. That’s the perfect start to his career here at Everton.”