The threat was made at 10:10 a.m. Monday by telephone against the building in the 5200 block of Hyde Park Boulevard, police said.
"Officers searched the building with staff and determined the threat was not bona fide," police said.
While police said the building was not evacuated, Alan Sataloff, the JCC's local CEO, told parents in an email that the building's staff was relocated to a "secure location" until police determined the threat was unfounded around 11:45 a.m.
"Everyone is safe and secure," Sataloff wrote.
With Chicago Public Schools students out of class to mark Presidents Day, children participating in the center's School's Out program were on a field trip when the threat was made, Sataloff said.
According to the Jewish Community Centers Association, 10 facilities received threats Monday, including the one in Chicago.
"While today is another instance of threats directed at JCCs across the county, none have been substantiated," Sataloff wrote. "This is a difficult time for our community, and we assure you that JCC Chicago locations are safe, and that we are open and operating as usual."
Since January, 53 Jewish Community Centers in 26 states have received threats, according to the Jewish Community Centers Association.
Mayor Rahm Emanuel called the recent wave of threats "cowardly" and "an affront to our most basic American values and shared sense of human decency" in a statement.
"Threats against any American are a threat to every American," Emanuel said.
A statement from the FBI said it is "investigating possible civil rights violations in connection with threats to Jewish Community Centers."