The medication was used in nearly two-thirds of all abortions in the United States last year.
The ruling is the court's first abortion decision since conservative justices overturned Roe v. Wade two years ago.
Justice Brett Kavanaugh, who was part of the majority to overturn Roe, wrote for the court that "federal courts are the wrong forum for addressing the plaintiffs' concerns about FDA's actions."
The case had threatened to restrict access to mifepristone across the country, including in states where abortion remains legal.
While the ruling drew praise from reproductive rights groups and many Democrats, some people suggested the fight over abortion rights and women's health care was not over.
U.S. President Joe Biden said the ruling "does not change the fact that the right for a woman to get the treatment she needs is imperiled if not impossible in many states."
Meanwhile, the attorney who represented anti-abortion doctors and their organizations in the case said the push to restrict abortion pills likely won't stop.