The highly-rated 19-year-old became the SPL's youngest ever goalscorer, with his strike against Hearts in 2010 and will now look to impress at the DW Stadium
Fyvie becomes Roberto Martinez's first signing of this summer's transfer window and the Latics' boss has expressed his delight at securing the deal.
He told Wigan's official website: "I'm excited because we're signing such a strong character and a great personality at just 19 years of age.
"He's got a tremendous future in his hands and we're all delighted that he's making a big step forward in his career here at Wigan Athletic.
"He's a bright young man and will have a good environment here in which to develop with players that have been through similar experiences and of course our fans who I know will make him feel very welcome and allow him to develop over the coming months."
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He became the youngest player ever to start for Aberdeen when he debuted against Hamilton Academical, and he went on to become the youngest ever goalscorer in Scotland's top-flight.
Martinez continued: "Technically he's very gifted, enjoys playing in the midfield where he can cover large areas, he's very powerful off the ball and in possession is someone who can read the tempo of the game very well.
"Also you have to remember that for such a young player he's played a lot of games in the SPL at a high standard which shows his maturity.
"Together with the rest of the squad and, of course, the other Scottish boys in the squad he'll settle in quickly I'm sure, but he's so eager to get going and take advantage of the good experience within the dressing room."