District Judge Matthew J Kacsmaryk, a Trump administration appointee in Amarillo, Texas, signed an injunction directing the Food and Drug Administration (FDA) to halt its approval while a lawsuit challenging its safety continues.
He sided, in part, with a conservative Christian group, Alliance Defending Freedom, who brought a lawsuit alleging the drug was not being regulated properly.
He did not go as far as the complainants wanted, but he put a "stay" or hold on approval of the drug.
The judge's decision does not come into effect for seven days. Meanwhile, the Department of Justice has announced it will appeal the ruling.
In a statement, President Joe Biden said: "My administration will fight this ruling...
"Let's be clear - the only way to stop those who are committed to taking away women's rights and freedoms in every state is to elect a Congress who will pass a law restoring Roe versus Wade.
"Vice President [Kamala] Harris and I will continue to lead the fight to protect a woman's right to an abortion, and to make her own decisions about her own health."