Health officials said the case was found in a person who is fully vaccinated and has received a booster dose. They have not required hospitalization and their health is improving, the Illinois Department of Public Health said.
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The patient had contact with an out-of-state visitor who tested positive for the omicron variant, and is self-isolating as they recover, officials said.
"We assumed that it was here, and now we've demonstrated that we can detect it," said Professor Stefan Green, with the Regional Innovative Public Health Laboratory at Rush University. "And now it's really kind of just a waiting game."
Health officials did not give the name of the Chicago resident nor the patient's gender.
Will COVID vaccines be effective against omicron variant?
Will COVID vaccines be effective against omicron variant?
More cases are likely to follow, including among those who have had contact with known omicron cases.
"We are following multiple individuals who we know had exposures, whether they were traveling in the U.S. or internationally," CDPH Commissioner Dr. Allison Arwady said.
It's behind-the-scenes lab testing that detects variants. Arwady said so far 99.9% of positive COVID cases in Chicago are still the delta variant.
SEE MORE: How severe is omicron? Expert says variant's 50 mutations could be its downfall
"It's kind of like a race between delta and omicron now," Green said.
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If omicron overtakes delta as the dominant variant, scientists at the University of Illinois at Chicago could be among the first to know. Their analysis of wastewater samples in 40 Illinois counties has provided context on how the virus is evolving.
"In a lot of places we see trends in upticks before we see the trends in clinical case data," said Professor Rachel Poretsky, with UIC Biological Sciences.
The variant's arrival comes as Illinois hospital beds are filling up.
Gov. JB Pritzker is working to increase access to at-home monoclonal antibody infusions in an effort to keep patients out of hospitals.
"But I'm hopeful what is now a surge of Delta variant that is filling our hospitals will abate," Pritzker said.
The city's effort to address omicron, as well as all other variants of the virus, is focused on testing and vaccination.
RELATED: Chicago prepares for arrival of Omicron variant; Lightfoot encourages COVID vaccination
The 11th floor of City Hall served as a Chicago Department of Public Health vaccination pop-up site Tuesday as the city continues to push everyone to get vaccinated and boosted.
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As the country begins to grapple with omicron, the Centers for Disease Control and Prevention has changed its guidance on home test kits, now urging anyone, even vaccinated people without symptoms, to use the rapid home tests before any indoor gatherings.
After Thanksgiving, CVS and Walgreens have seen a big uptick in the sale of home test kits. They run about $23.00 a box, but the Biden Administration has stated a goal to provide them to everyone for free. Until that happens, the city of Chicago plans to increase the availability of free home kits.
Whether it's a home rapid test or PCR, Dr. Arwady said neither is able to detect what variant you may have.
"When you get a test, whether it's an antigen test or a PCR test, the answer it gives you is yes/no; I have COVID or do not," she explained.
The World Health Organization said early data show omicron may be more transmissible than delta, but may not cause more severe illness. Health officials say more data is still needed to be sure.