The Supreme Court case related to federal law limiting gun ownership for people convicted of domestic violence.
Justice Thomas has said in the past he prefers not to "badger" lawyers as they present their arguments in court.
He spoke weeks after the death of one of the most conservative Supreme Court members, Justice Antonin Scalia, which may shift the court's balance of power.
Justice Thomas on Monday asked a lawyer for the Department of Justice whether the violation of any law "suspends a [person's] constitutional rights".
The court is considering placing new limits on the reach of the federal law banning people convicted of domestic violence from owning guns.
It was the court's second week of oral arguments - when justices are given the chance to question lawyers about their briefs - since the death of Justice Scalia, a friend and fellow conservative of Justice Thomas.
The last time he was reported to have asked a question at the high court was during a death penalty case in February 2006.
Explaining his silence over the years, Justice Thomas told the Associated Press in 2013: "We have a lifetime to go back in chambers and to argue with each other."
He told a group of students in 2000 that "there's no reason to add to the volume. I also believe strongly, unless I want an answer, I don't ask things... Usually, if you wait long enough, someone will ask your question".