Jeremy Halbreich replaces Cyrus Freidheim, whose resignation is effective Feb. 28.
Halbreich says the company's current managers will stay in place to give them "the time and resources to charge ahead."
Officials on Wednesday also named the company's current general manager, John Barron, as publisher and Rick Surkamer as president and chief operating officer.
Sun-Times Media publishes the Chicago Sun-Times and area community papers.
The company has made cuts due to declining advertising revenue. Last month, it closed 12 weekly newspapers and asked union employees to take cuts in compensation.