The 19-year-old is currently with the City squad on their pre-season tour of the USA, but the Welshman is expected to join up with Championship club Wigan before the start of the season.
Huws scored twice in 17 appearances while on loan at Birmingham City last season, and his goal against Middlesbrough won the club's Goal of the Season award.
Wigan boss Uwe Rosler told Athletic's website: "City are looking for Emyr to develop and as we have demonstrated in the past, top young players are able to come to us and improve, both on the field with regular playing time, but also off the field in terms of absorbing our first-team training culture and discipline and helping them to improve every facet of their professional life.
"He is a very exciting player, I know him after working with him during a short spell I spent at City's Academy in 2010-11 and he is clearly a very talented young player who has already broken through to the national squad, plus has played in the Championship.
"He is a silky left-footer, versatile, who can dictate play with his passing, but who does not shy away from the physical demands of the Championship."