City officials said the school closures would affect approximately 30,000 children, mostly in kindergarten through eighth grade.
Emanuel has prodded officials for months to work on the downsizing of the school district to help soften the blow of next year's deficit, the Chicago Tribune reported Thursday.
"We have resources that are spread much too thin," said Todd Babbitz, the district's chief transformation officer.
The closures, and upgrades of remaining schools to handle the influx of new students, are expected to initially cost the city $233 million, though the district projects a savings of $560 million over the next decade.
Anxious parents expressed concern over students' displacement and potentially longer and more dangerous walks to a new school, the Tribune reported.
Some youngsters were worried, too.
"People there may be fighting," said fourth-grader Jayshawn Vinson, who will have to walk an additional mile to school over the busy Martin Luther King Drive. "They may be shooting. I don't know what will happen in the neighborhood."