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".

Sir Neville started his musical career with the London Symphony Orchestra.
He later established the Academy of St Martin in the Fields, one of the world's leading chamber orchestras.
Its chairman, Paul Aylieff, said Sir Neville's artistic and recording legacy with orchestras and audiences worldwide was "immense".
"He will be greatly missed by all who knew and worked with him and the academy will ensure it continues to be an excellent and fitting testament to Sir Neville," Mr Aylieff added.
A statement from the academy said its founder had passed away peacefully in the early hours of Sunday.
Born in Lincoln in 1924, Sir Neville studied at the Royal College of Music and the Paris Conservatoire.
He first played in a string quartet, then in the London Symphony Orchestra, during which time he decided to form a chamber ensemble from London's finest players.
A group of friends began rehearsing in Sir Neville's front room, before taking their name from the London church of St Martin in the Fields where they staged their first performance in 1959.
The academy, which Sir Neville became life president of, says it now has one of the largest collections of recordings of any chamber orchestra in the world.
Sir Neville has been widely honoured for his work which includes recording the soundtrack for the 1984 film, Amadeus, and becoming the oldest conductor to lead at the Proms, in 2014 at the age of 90.
In March, he was made a Companion of Honour by the Duke of Cambridge at Buckingham Palace, and has also been honoured in France, Germany and Sweden.

It happened at the Moelfre Lifeboat open day at 16:10 BST on Saturday, with two RNLI vessels rescuing him.
He was then taken to Ysbyty Gwynedd, Bangor, by a UK Coastguard helicopter, with his condition unknown.
North Wales Police is investigating the incident and has appealed for witnesses.
Organisers had earlier warned about safety in the water on its Facebook page, imposing a speed restriction on boats travelling to the event.
They had said: "From past experience, we are expected to have over 100 vessels.
"Some will be kayaks with children on board, water safety is very important. Many adults and children will be swimming in the bay. Keep your eyes peeled please."
The event, at the RNLI station, was to allow people to meet the crew and celebrate their life-saving work.

The county council plans to build 200 council homes and 300 affordable homes.
The first will be built on the site of the former Custom House Lane School in Connah's Quay.
Meanwhile, the nearby "old dairy" on Mold Road is being flattened along with some terraced homes on the adjacent High Street. The former dairy has stood empty for more than 30 years.
The council has asked experts to draw up proposals for the site, which will be levelled and seeded once demolition work is completed in March.
Justice Clarence Thomas, one of eight judges at the highest court in the US, has broken a 10-year silence at court.
[NEXT_CONCEPT]
The British conductor and violinist, Sir Neville Marriner, has died at the age of 92, the Academy of St Martin in the Fields says.
[NEXT_CONCEPT]
A jet skier has been airlifted to hospital after a crash involving a speedboat during an event off Anglesey.
[NEXT_CONCEPT]
Building work is due to start next month on the first new council homes in Flintshire for more than 20 years.