Democrats in the state had asked the court to allow the counting of ballots that arrive up to six days after Election Day if they were postmarked by November 3.
The ruling was 5-3, coming just before the Senate voted to add Judge Amy Coney Barrett to the Supreme Court.
Justice Elena Kagan, joined by her liberal colleagues, Justices Sonia Sotomayor and Stephen Breyer, dissented from the court's order.
Last week, the court had upheld a ruling by a state court in Pennsylvania extending the mail-in ballot deadline there.
Difference between Pennsylvania and Wisconsin cases
Monday's order is the latest sign that the justices do not want federal courts to change voting rules too close to the election.
Unlike the Pennsylvania order last week, the Wisconsin order Monday concerned a ruling from a lower federal court, not a state court, and Chief Justice John Roberts said that made a difference.
A federal district court in Wisconsin had sided with the Democrats to allow mail-in ballots to be received up to six days after Election Day, but an appeals court blocked that order and the Supreme Court upheld the block.
The federal district court, Roberts wrote in a concurring opinion, "intervened in the thick of election season" to block a state law. He said the case represented "federal intrusion on state lawmaking processes."
The Pennsylvania case, on the other hand, concerned a decision by the state's highest court. Roberts said that decision "implicated the authority of state courts to apply their own constitutions to election regulations."
"Different bodies of law and different precedents govern these two situations and require, in these particular circumstances, that we allow the modification of election rules in Pennsylvania but not Wisconsin," Roberts wrote.
It's unclear how long the court will make that distinction now that Barrett is joining as the ninth member, said Steve Vladeck, CNN legal analyst and professor at the University of Texas School of Law.
"The only justice to view these cases differently than the ones from Pennsylvania was the Chief Justice, for whom there's apparently a categorical difference between a state Supreme Dourt extending election deadlines, which he refused to upend, and a federal district court doing the same," Vladeck said. "But the central role of the Chief Justice may well be short-lived with Justice Barrett presumably able to vote on the next set of election cases.
This story is breaking and will be updated.