The Supreme Court ruled on Wednesday that the Food and Drug Administration had acted lawfully in rejecting applications from two manufacturers of flavored liquids used in e-cigarettes with names like Jimmy the Juice Man Peachy Strawberry, Signature Series Mom’s Pistachio and Suicide Bunny Mother’s Milk and Cookies.

In a unanimous decision written by Justice Samuel A. Alito Jr., the justices upheld an F.D.A. order that prohibited retailers from marketing flavored tobacco products. The court rejected claims that the agency had unfairly switched its requirements during the application process.

Justice Alito wrote that the agency’s denials of the applications were “sufficiently consistent” with agency guidance on tobacco regulations. The justices rejected a ruling by the U.S. Court of Appeals for the Fifth Circuit that the agency had acted arbitrarily and capriciously, finding that the F.D.A. had not tried to change the rules in the middle of the approval process.

In the opinion, Justice Alito highlighted the possible dangers of the flavored products appealing to middle and high school students, writing that “the kaleidoscope of flavor options adds to the allure of e-cigarettes and has thus contributed to the booming demand for such products among young Americans.”

“Flavors lure kids, which is why Congress gave F.D.A. the authority to make science-based decisions on what is appropriate for our nation’s health,” said Erika Sward, the assistant vice president for nationwide advocacy at the American Lung Association, who applauded the court’s ruling.

The decision comes at a fraught turning point for the agency.

In recent months, leaders celebrated a 10-year low in the percent of adolescents using e-cigarettes. The F.D.A. has attributed the decline to effective messaging targeted at teenagers and to aggressive enforcement against those who market illicit vapes in flavors like Unicorn Shake and watermelon bubble gum.

The agency is also grappling with deep cuts to its tobacco division staff and its counterpart at the Centers for Disease Control and Prevention, which gathers data on youth tobacco use. Amid thousands of staff cuts, Brian King, the director of the F.D.A.’s Center for Tobacco Products, was offered a new role in the Indian Health Service, with the option to work in Alaska or New Mexico — a tacit ouster.

Ms. Sward described the decimation of the federal tobacco control staff as “Christmas Day for big tobacco.”

“There is no one to keep the tobacco industry from flooding the market with its deadly products and no one left to count how many kids they addict,” she said.

The decision on Wednesday is a “ringing validation” of the F.D.A.’s work, said Mitch Zeller, a former director of the agency’s tobacco division who served during the first Trump administration and under Presidents Barack Obama and Joseph R. Biden Jr. But he said its timing — a day after the deep cuts — was ironic and boded poorly for the future of limiting youth tobacco use.

“The Trump administration’s destruction of the Food and Drug Administration and the Center for Tobacco Products, in particular, imperils the ability of the center to continue to do its job on behalf of the public health,” he said.

A 2009 law, the Family Smoking Prevention and Tobacco Control Act, requires makers of new tobacco products to obtain authorization from the F.D.A. According to the law, the manufacturers’ applications must demonstrate that their products are “appropriate for the protection of the public health.”

The agency has denied many applications under the law, including the two at issue in the case before the justices, saying the flavored liquids presented a “known and substantial risk to youth.”

The appeals court ruled last year that the agency had changed the rules in the middle of the application process, accusing it of “regulatory switcheroos” that sent the companies “on a wild-goose chase.” More formally, the court said the agency’s actions had been arbitrary and capricious.

In asking the Supreme Court to hear the case, Food and Drug Administration v. Wages and White Lion Investments, No. 23-1038, the agency’s lawyers cited another appeals court that had reached the opposite conclusion. The Fifth Circuit’s decision “has far-reaching consequences for public health and threatens to undermine the Tobacco Control Act’s central objective of ‘ensuring that another generation of Americans does not become addicted to nicotine and tobacco products,’” they wrote, quoting from the other appeals court’s decision.

What’s next for federal tobacco regulation is uncertain. President Trump has suggested that he will advance the interests of adults who use e-cigarettes, many of whom also use flavored vapes.

Major tobacco companies, though, have complied with F.D.A. rules and gotten approval to sell more staid products, including tobacco and menthol-flavored e-cigarettes. At least one company, Reynolds American, has donated heavily to Mr. Trump’s campaign and has made it clear that it wants the F.D.A. to crack down on the flavored e-cigarettes pouring in from China and taking away its market share.