Yes. Anwar al-Awlaki was a United States citizen targeted and killed by a missile strike. The NY Times writes:
In 2010, the Obama administration had taken the rare step of authorizing the targeted killing of Mr. Awlaki, even though he was an American citizen — a step that had provoked lawsuits and criticism from human rights groups.
Although technically a covert operation, this article discusses the authorizing memo, saying,:
The secret document provided the justification for acting despite an executive order banning assassinations, a federal law against murder, protections in the Bill of Rights and various strictures of the international laws of war, according to people familiar with the analysis. The memo, however, was narrowly drawn to the specifics of Mr. Awlaki’s case and did not establish a broad new legal doctrine to permit the targeted killing of any Americans believed to pose a terrorist threat.