England Under-21 international Cleverley's loan spell at Watford was ended last season when he suffered knee ligament damage against West Bromwich Albion in April.
He had looked set to stay at Old Trafford this season after impressing in Manchester United's pre-season games with performances which led United boss Sir Alex Ferguson to compare him to Paul Scholes.
But Cleverley will now be handed the chance to gain Premier League experience with Wigan.
Martinez added: "We have been watching him for some time and feel he is the right sort of player to join our squad; young, hungry, desperate to play for the club in the Premier League and to grow with us."
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