The EPA has required states since January 2 to begin issuing greenhouse gas permits for the biggest polluters, such as oil refineries, coal-burning power plants, cement and glass makers.
Texas, home to hundreds of plants that would be subject to the regulations, said the rules would hurt its economy.
The EPA said it would issue permits for Texas, but ahead of a ruling on the case Texas asked for a delay of the agency's actions.
The U.S. Court of Appeals for the District of Columbia denied the delay. It said the state had "not satisfied the stringent standards required for a stay pending court review."
One environmentalist applauded the ruling.
"Three strikes should mean 'you're out' in this case," said Steve Cochran, a vice president for climate and air at the Environmental Defense Fund.
"If Texas put half the effort into carrying out greenhouse gas pollution control measures that it put into fighting them, EPA would not need to be involved. Plus, Texas businesses could then enjoy the same certainty that businesses in every other state will have," he said.
The EPA said in a release the court's move "ensures that our efforts to enact modest, common-sense steps to address carbon pollution under the Clean Air Act... will proceed in the state of Texas just as they are proceeding across the nation."
"We look forward to working with Texas officials to ensure that their industrial facilities can seek permits to expand and grow while protecting the health of all Texans," the EPA said.
The Texas Commission on Environmental Quality said it was dismayed by the ruling.
"The TCEQ is disappointed in this decision, but confident we will ultimately prevail in our insistence that the EPA must follow its own rules and federal law, and that environmental regulations must have some environmental benefit, and not just expand the power of the federal government," the agency said in a statement.