Based solely on the progression of Magneto's storyline, I think we can safely assume it takes more than one day. There's also a few places where I suspect we're supposed to mentally insert "the next day..." into a scene. As a gut feeling I would say 3 days, though there are not very many clues.
Magneto's story definitely takes place over the course of at least two days. On day 1, he is at work when there is an accident, and he's forced to use his powers to save a coworker. He returns home at the end of his shift, puts his daughter to bed, and starts preparing to run. After he's confronted by the lynch mob, he returns to his place of work the next day to kill everyone, where he joins Apocalypse and the others.
Magneto's accident was caused by Apocalypse, probably within hours of his waking up, so we know Apocalypse also woke up on day #1 and came to meet Magneto on day #2.
Also on day #1, when Apocalypse woke up, Moira was in Egypt during the afternoon, when she discovered his tomb. She then goes back to Washington DC to her office where she meets with Xavier. Given the flight time and time difference, and the fact that Moira appears to be rested/cleaned-up/etc, this must be the next day, the same day Magneto and Apocalypse meet.
On that same day #2, the 3 students sneak off to spend the day at the mall, and they are still gone when Xavier gets back to the mansion. Apocalypse abducts Charles and blows up the rest of the mansion in the process, and Stryker shows up just as the kinds are coming back from the mall. So, all of this must have been happening on the same day, day 2.
From there things moved pretty fast, as there's not much of a break in the action. The adult X-Men are captured and held by Stryker, the younger ones rescue them, and they immediately head for Egypt and Xavier for the final confrontation. however, that Egypt is 7 hours ahead of DC, so the fact that it was midday in Egypt when they arrived means it's likely another night has passed, and it was now early morning of Day 3 in New York when the climactic battle happened.