The U.S. Supreme Court ruled 6–2 (Justice Field did not participate for obvious reasons) that Neagle should be free of the charges because he was acting in his capacity as a U.S. marshal providing protection to a federal judge. In his majority opinion, Justice Samuel Miller noted the unusual circumstances, writing: “The occurrence which we are called upon to consider was of so extraordinary a character that it is not to be expected that many cases can be found to cite as authority upon the subject.” The Court determined that Neagle was entitled to federal habeas relief because he was acting under the authority of the U.S. government. “Why do we have marshals at all, if they cannot physically lay their hands on persons and things in the performance of their proper duties?” Miller wrote. “What functions can they perform, if they cannot use force?”

Justice Lucius Lamar and Chief Justice Fuller dissented, though not on any “conviction as to the guilt or innocence” of Neagle. These justices reasoned that the federal courts did not have jurisdiction over this situation.