CPD said Jones College Prep, which is operated by Chicago Public Schools and is located at 700 S. State St., was one of the schools involved.
Police said multiple 911 calls came in about 2:05 p.m. about a bomb threat and a person with a gun at the school.
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Police and SWAT teams swept every floor of the school, but the threat was deemed not credible.
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CPD said there is no threat to students.
They called the incident swatting, in which a threatening call is made to prompt a SWAT response.
Students were released later Wednesday afternoon, much to the relief of many parents who came to pick up their children.
The parents said they were glad no one was hurt.
About 3:30 p.m., there was a large police presence outside the South Loop high school, blocking roads.
In a letter to families, Jones College Prep said a threat was received via email, and the school was placed on hard lockdown.
"I am extremely thankful for our students and staff. Despite the fact that this proved to be a baseless threat, this incident was frightening for many of us, and the way in which your students and our staff carried themselves, looked out for one another, and followed procedures made me and our team extremely proud," the letter from the principal said.
After-school activities were still expected to take place.