Walton was abducted by suspected bandits on October 26 in Niger Republic.
According to ABC News, the operation involved the governments of the U.S., Niger and Nigeria working together to rescue him quickly.
It said the elite SEAL Team Six carried out the rescue mission and killed all but one of the captors, according to officials with direct knowledge about the operation.
"They were all dead before they knew what happened," another counterterrorism source with knowledge told ABC News.
The Pentagon lauded the rescue mission in a statement.
“U.S. Forces conducted a hostage rescue operation during the early hours of 31 October in Northern Nigeria to recover an American citizen held hostage by a group of armed men," said Pentagon chief spokesperson, Jonathan Hoffman.
"This American citizen is safe and is now in the care of the U.S. Department of State. No U.S military personnel were injured during the operation.
"We appreciate the support of our international partners in conducting this operation."
U.S. and Nigerien officials had said that Walton was kidnapped from his backyard last Monday after assailants asked him for money.
But he only offered $40 and was then taken away by force, according to sources in Niger.
Walton lives with his wife and young daughter on a farm near Massalata, a small village close to the border with Nigeria.
Nigerien and American officials told ABC News that they believed the captors were from an armed group from Nigeria and that it was not considered terror-related even though hostages are often sold to terror groups.
Concern grew quickly after the kidnapping that an opportunity to rescue Walton could become much more dangerous if he was taken by or sold to a group of Islamist militants aligned with either al Qaeda or ISIS and American special operations commanders felt they needed to act swiftly before that could occur, said one counterterrorism official briefed on the hostage recovery operations.
A U.S. State Department spokesperson confirmed after the kidnapping that an American citizen had been abducted in Niger and said the U.S. Government was "providing their family all possible consular assistance."
The spokesperson declined to comment on the case, citing "privacy considerations," but added, "When a U.S. citizen is missing, we work closely with local authorities as they carry out their search efforts and we share information with families however we can."