The court voted 2-1 to overturn a lower-court ruling that would have kept his name on the Feb. 22 ballot. Emanuel plans to appeal the matter to the Illinois Supreme Court. Early voting was set to begin on Jan. 31.
"I have no doubt that we will in the end prevail at this effort. This is just one turn in the road," said Emanuel. "The people of the city of Chicago deserve the right to make the decision on who they want to be their next mayor."
Those challenging Emanuel's candidacy have argued that the Democrat does not meet the one-year residency requirement because he rented out his Chicago home and moved his family to Washington D.C. to work for President Barack Obama for nearly two years. Emanuel has said he always intended to return to Chicago and was only living in Washington at the request of the president.
Emanuel is one of several candidates vying to replace Chicago Mayor Richard Daley, who did not seek a seventh term. Emanuel moved back to Chicago last October after he quit working for Obama to campaign full-time.
The Chicago Board of Election Commissioners and a Cook County judge have both ruled in favor of Emanuel, a former congressman, saying he didn't abandon his Chicago residency when he went to work at the White House.
Emanuel appeared to have gotten a big boost last week when his campaign announced he raised more than $10 million and was endorsed by former President Bill Clinton during an event in Chicago.
A Chicago Tribune/WGN poll also released last week showed Emanuel with the support of 44 percent of those surveyed.