Felix Kulaigye, a spokesman for the Ugandan military, described Ceasar Achellam as a "big fish" in the LRA.
"His capture is definitely going to cause an opinion shift within LRA," Kulaigye was quoted by the BBC as saying.
Achellam, who said he's been fighting in the jungles for nearly 30 years, confirmed his arrest.
"My coming out will have a big impact for the people still in the bush to come out and end this war soon," he was quoted as saying.
The BBC said Achellam was arrested last weekend following a brief skirmish between the Ugandan military and around 30 rebels. He was reportedly captured in the Central African Republic.
The BBC estimated there are around 300 active LRA fighters in the region. LRA leader Joseph Kony remains at large despite a 2005 indictment by the International Criminal Court on more than 30 counts of violations of international law, including war crimes.
The White House announced in April that U.S. military advisers would be deployed in Uganda to help track down members of the LRA. It was unclear if the advisers played a role in the capture of Achellam.