A group representing families of Japanese abductees to North Korea confirmed Mr Jenkins died on Monday after he was found collapsed outside his home in Sado, northern Japan.
Japan's NHK national television said he died of a heart failure.
He and three other American soldiers disappeared in 1965 while patrolling along the Demilitarized Zone (DMZ) dividing North and South Korea.
Once in Japan, Jenkins in 2004 was subject to a USA court-martial in which he said he deserted because of fear of being sent to fight in Vietnam.
The life of ex-US Army sergeant Charles Robert Jenkins as a defector to North Korea reads like dramatic novel. I started to drink alcohol. I looked at her one time.
After drinking 10 beers, Mr Jenkins took his men on patrol and told them to wait while he checked the road below. He then walked towards North Korea, holding a rifle with a white T-shirt tied around it. Jenkins said he did his best to make her feel safe, protected and respected and they eventually bonded over their loneliness and their mutual hatred of North Korea. He also taught English to soldiers and played the role of evil United States spy in movies.
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He later called his desertion a mistake that led to decades of deprivation and hardship in the communist country.
James Joseph Dresnok, the only USA soldier known still to have been living in North Korea after defecting more than five decades ago, died in November 2016, his sons confirmed in August.
Fear for his safety and the family he built with his wife made it impossible to refuse any demands made on him, he said in 2004.
'You don't say no to North Korea. "You say one thing bad about Kim Il-sung and then you dig your own hole, because you're gone", Jenkins said during his court-martial.
Jenkins met his wife Hitomi Soga, who was kidnapped by Pyongyang in 1978, in North Korea and the couple had two daughters, Mika and Blinda.
The Japanese government granted him permanent residency and he lived in Soga's hometown on Sado, a picturesque island in the Sea of Japan.
He subsequently worked in a gift shop and wrote a book about his experiences in North Korea.