Athletic director Dave Blank announced the hiring Thursday.
Skrosky was on Pete Lembo's staff at Elon from 2006-10 before following him to Ball State, where he spent the past three seasons as the Cardinals' offensive coordinator and quarterbacks coach.
Ball State (10-2) averaged 486 yards and 40 points this season, beat Virginia by three touchdowns and earned a berth in the GoDaddy Bowl.
Skrosky says he is ''returning to a place that is very special'' to him.
He replaces Jason Swepson, who was fired Nov. 25 after going 10-24 in three seasons.
The Phoenix will begin play in the Colonial Athletic Association in 2014 after competing in the Southern Conference since 2003.
• Elon fires Swepson after three seasons