Judge Collyer cited officials’ statements that Mr. Awlaki was a terrorist leader with the Yemeni group known as Al Qaeda in the Arabian Peninsula. She also cited an account of his role in a plot to blow up a Detroit-bound jet in 2009, based on court documents from the trial of a Nigerian man who pleaded guilty to trying to bomb the plane, and statements by Mr. Awlaki praising and encouraging acts of terrorism.

Nasser al-Awlaki, the father of Anwar and grandfather of Abdulrahman, and Sarah Khan, Mr. Khan’s mother, filed the lawsuit in July 2012 against several officials it accused of authorizing and directing the strikes, including the secretary of defense and the director of the C.I.A. It did not name the president, who is immune from such lawsuits.

Nasser al-Awlaki had filed a lawsuit in 2010 seeking an injunction to stop attempts to kill his son, but another Federal District Court judge, John D. Bates, dismissed the case on the grounds that Mr. Awlaki had no standing to bring it on behalf of his son. In the second lawsuit, Mr. Awlaki was acting as the executor of his son’s and grandson’s estates.

In May 2013, the Obama administration declassified and formally acknowledged the fact that it had killed the three men. It argued that the case should be dismissed without any further evidence before the court. Judge Collyer agreed, saying that allowing the plaintiffs to pursue the case would “impermissibly draw the court” into executive deliberations about how to protect national security.

“The Constitution commits decision-making in this area to the president, as commander in chief, and to Congress,” she wrote, adding that allowing a lawsuit against top government officials would “hinder their ability in the future to act decisively and without hesitation in defense of U.S. interests.”

Judge Collyer was appointed to Federal District Court in 2002 by President George W. Bush. Last year, Chief Justice John G. Roberts Jr. selected her to serve a term on the Foreign Intelligence Surveillance Court, which oversees government spying on American soil, filling a seat previously held by Judge Bates.

The Obama administration is separately fighting Freedom of Information Act lawsuits brought by The New York Times and the American Civil Liberties Union seeking disclosure of a classified Justice Department memo explaining its legal reasoning for the strike, although an unclassified “white paper” summarizing those arguments has become public.