The reversal comes after withering criticism from the Chicago Teachers Union, though officials say they made the decision after they "evaluated the situation again."
City officials said earlier Sunday that schools would be open on Monday, but parents could choose to keep their children home.
Temperatures were expected to dip to minus 15 degrees on Monday, with wind chills of 40 to 50 below zero possible. The city also was walloped by snow on Sunday.
City emergency officials had warned residents to stay indoors on Monday. Many Chicago students must walk to school.
Chicago Schools CEO Barbara Byrd-Bennett says closing is "in the best interest of our students."