The families of the three, including New Mexico-born militant cleric Anwar al-Awlaki, sued over their deaths, arguing that the killings were illegal.
Judge Rosemary Collyer of the U.S. District Court in Washington threw out the case.
"The question presented is whether federal officials can be held personally liable for their roles in drone strikes abroad that target and kill U.S. citizens," Collyer said in her opinion. "The question raises fundamental issues regarding constitutional principles, and it is not easy to answer."
But the judge said she would grant the government's motion to dismiss the case.
Collyer said that the U.S. officials named as defendants in the case "must be trusted and expected to act in accordance with the U.S. Constitution when they intentionally target a U.S. citizen abroad at the direction of the president and with the concurrence of Congress. They cannot be held personally responsible in monetary damages for conducting war."
Lawyers for the families had argued that in killing American citizens, the U.S. government had violated fundamental rights under the Constitution to due process and to be free from unreasonable seizure.