The emergency request was brought by a man who said a generalized anxiety disorder prevented him from wearing a mask and he was unable to board a flight leaving Orlando, Florida, last month, the Washington Examiner reported.
Lucas Wall, a frequent flier from Washington, D.C., called Thomas’s decision "disappointing" while acknowledging the Monday request had been a "long shot."
"Of course it's still disappointing Justice Thomas did not take a more in-depth look at the illegal and unconstitutional mask requirement," he said.
Thomas oversees appeals from Florida. He gave no explanation for his decision.
The court has been open to lifting pandemic-era orders, especially religious gathering restrictions. In April, the court ruled California must allow in-home religious meetings.
Wall said he thought the court’s 5-4 ruling to keep the federal eviction moratorium last month meant the justices might be open to removing the mask mandate.
He called the policy issued by the Biden administration earlier this year "improper, illegal, and unconstitutional."
"For now, the federal government has prevailed in muzzling all travelers and banning tens of millions of Americans including myself who can't tolerate having their face covered from using any form of public transportation," Wall said, adding he still thinks he will win his case, according to the Examiner.
He is suing President Biden, the Centers for Disease Control & Prevention, the Transportation Security Administration, and 5 other defendants, according to a fundraising page.
On Wednesday, U.S. Sen. Rand Paul, R-Ky., introduced legislation to remove the transportation mandate.
The bill would prohibit federal agencies from imposing "any federal requirement related to COVID-19 that an individual wear a face mask when utilizing any conveyance…or transportation hub."
Paul told Fox News, "The federal government forcing the American people to continue to wear masks despite the fact that we’ve already reached herd immunity is ridiculous and needs to end immediately. I am introducing the Travel Mask Mandate Repeal Act of 2021 to put a stop to this nanny state mandate of requiring masks on public transportation."
Fox News' Brooke Singman contributed to this report.