The Court voted 2-1 to issue a stay on an order that had banned US Department of Agriculture inspections at the slaughterhouse.
Without the inspectors, the DeKalb plant is unable to operate. The order will allow resumption, at least for now.
The Humane Society of the United States, which opposes slaughter, registered its disappointment over the decision.
However, the slaughter industry remains under attack on several fronts, with proposed laws working their way through Illinois and Federal houses in a bid to bring the industry to a final close in the US.
Until recently, three plants have been operating in the US, slaughtering more than 100,000 horses a year. The meat is exported for human consumption.
Two plants were forced to close in Texas after a court ruling confrimed a state ban on slaughter. That left the Illinois plant at DeKalb, owned by the Belgian company Cavel International, still in operation.
That plant was forced to close only weeks ago when a Federal court ruling stopped the US Department of Agriculture providing mandatory inspections, for which the plant paid.
However, the May 1 ruling granted the slaughterhouse's emergency request to resume killing while it considers an appeal of a March lower-court ruling that halted the federal inspection.
The plant had argued before the court that it could go out of a business if it did not get a stay - an argument that one judge did not accept, pointing out that the plant had once withstood a two-year shut-down following a fire.
Anti-slaughter lobbyists consider the legislation pending in Congress to be the key to bringing slaughter to a final close. The bill would not only end slaughter, but prevent horses being taken across US borders to plants in Mexico and Canada.