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The court's action is one of only a handful of such "emergency docket" cases in which the conservative court has ruled against Trump since he began his second term as president almost a year ago.
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Many legal experts thought this emergency decision would take days or weeks, not months, as ended up being the case.
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It's unclear why it took so long.
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It's the first time the highest court has weighed in on the controversial deployments.
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While the decision does not set precedent, it brings some clarity about the president's power to deploy federal military resources.
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But for all practical purposes, the president for now at least, cannot send in National Guard troops in Illinois without the governor's permission.
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The White House did not immediately respond to a request for comment from NPR.
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The administration withdrew many of its law enforcement forces from Chicago in November and moved them to New Orleans and Minneapolis, as it launched new immigration crackdowns in those locations, but recently moved many back to Chicago and redoubled efforts in the city.
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Local and state officials in Illinois have condemned the troop deployments, calling them unnecessary and accusing the president of overstepping his authority.
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Republican Texas Gov. Greg Abbott also sent 200 of his state's National Guard troops to help.
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They returned to Texas in November, after waiting for weeks while the deployment was blocked by the courts.
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Repeated legal setbacks
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The deployments have faced other legal setbacks.
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In Oregon, a federal judge earlier blocked a deployment in Portland, finding that Trump "did not have a lawful basis to federalize the National Guard" and doing so violated states' sovereignty, member station OPB reported.
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The Trump administration is challenging the ruling, but recalled hundreds of troops from the state.
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Troops have been deployed in Memphis since October, where Tennessee Republican Gov. Bill Lee welcomed federal intervention.
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In November, a state judge temporarily blocked the use of troops, but that ruling was paused after the state appealed, The Associated Press reported.
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In June, Trump seized control of California's National Guard against Gov. Gavin Newsom's wishes and deployed thousands of troops to Los Angeles in response to protests over immigration raids in the city.
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The administration then sought to extend that federalization and deployment several times, keeping around 100 troops in the city, until a federal judge ruled it had to end in December.
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A federal appeals court agreed, and troops were ordered out of Los Angeles.