The deposition is scheduled for April 4 in Indianapolis, two weeks before the trial in the long-running case is scheduled to begin.
At issue are Emmert's comments to USA Today in December 2010: "Everybody looks at the Reggie Bush case and says, 'It took them a long time.' But they got it right, I think."
In a court filing last month, McNair's legal team described the comments as part of the "character assassination of Mr. McNair."
Shaller didn't agree. The judge is a USC graduate who the NCAA unsuccessfully tried to remove from the case in 2016.