A judge in Florida struck down the mask mandate for airplanes and other forms of public transit, saying it was illegal.
The national public health agency exceeded its legal powers in issuing the mandate according to the US District Judge.
The mandate was extended last week by the CDC.
The transit authority in the US will no longer enforce masks.
Federal judges can issue rulings that block government policies.
The masking requirement in airports, trains, taxis and transit hubs has been removed by her order on Monday.
The decision was disappointing and the CDC still recommends that travellers cover their mouths and noses.
The CDC did not immediately respond to the request for comment.
The mandate was extended into May because of rising Covid-19 cases, according to the US Surgeon General.
The Health Freedom Defense Fund and two Florida residents brought the first lawsuit in July of 2021.
The CDC mandate was argued to bearbitrary and capricious because it gave exemptions to certain groups, like children under two years of age.
The CDC was found to have violated the good cause exception by skipping public notice and comment on the mandate.
The judge wrote that the system does not allow agencies to act illegally even in pursuit of desirable ends.
A Biden administration official said that the Transportation Security Administration would no longer enforce the mask mandate after the legal decision was issued.
More than 7,000 unruly passenger incidents have been reported since the CDC issued a public health order requiring masks for travellers in February of 2021, according to the Federal Aviation Administration.
The Covid-19 mandates have had mixed success in the court system.
The White House's vaccine-or-test rule for employees of large private companies was blocked by the Supreme Court.
The Biden administration's requirement that all federal employees bevaccinated against Covid-19 was upheld on appeal.