The redshirt senior was competing with redshirt freshman Deondre Francois for the starting job after Maguire split time as the starter last season. He lost the job to Everett Golson at the start of the 2015 season but ended up starting five games.
He suffered the injury Wednesday during the second practice of camp and will likely have surgery Monday.
"On the [right] foot, the outside little bone in his foot, they're going to have to put a screw in it," Fisher said. "The same injury [safety] Derwin [James] had, so [Maguire will be out] about four weeks. He'll be back probably by the second, third game of the year."
Fisher said he will not name Francois the starter, but he said the 6-foot-2, 205-pound Francois is "definitely" the No. 1 quarterback as it stands. The Seminoles open the season Sept. 5 against Ole Miss in Orlando, Florida, then play Charleston Southern five days later.
"Some good, some bad, but I'm pleased. I'm not unhappy at all, about where I thought," Fisher said of Francois' play through the first week of practice. "And we're mixing and matching with different offensive line sets, different backfields, different receiver groups. There's a mix-and-match time. You'll have time to hone things [in later practices]."
Francois redshirted last season as a true freshman. He was No. 42 in the 2015 ESPN 300, and he was the third-ranked dual-threat quarterback. He spent his senior season at the IMG Academy. He has never thrown a pass in a college game.
"I don't know. I don't know yet," Fisher said when asked if Francois is ready to be the starter. "It isn't the game yet. When it gets to the game, we'll see."
In the Chick-fil-A Peach Bowl on New Year's Eve, Maguire fractured his left ankle in the first quarter. He returned to the game, but the injury required surgery. He missed all of spring practice.
As a junior, he threw for 1,520 yards, 11 touchdowns and six interceptions. In 2014, he started in place of Jameis Winston for the No. 1 Seminoles against Clemson and helped lead an overtime win.
"There's somebody with as much character as anybody on our football team," Fisher said. "Of course he's down. He felt bad, but there was no hesitation about what to do and how to do it. I have the utmost respect for Sean Maguire."