Hiroo Onoda remained in the jungle on Lubang Island near Luzon, in the Philippines, until 1974 because he did not believe that the war had ended.
He was finally persuaded to emerge after his ageing former commanding officer was flown in to see him.
Correspondents say he was greeted as a hero on his return to Japan.
As WWII neared its end, Hiroo Onoda, then a lieutenant, became cut off on Lubang as US troops came north.
The young soldier had orders not to surrender – a command he obeyed for nearly three decades.
“Every Japanese soldier was prepared for death, but as an intelligence officer I was ordered to conduct guerrilla warfare and not to die,” he told ABC in an interview in 2010.
“I became an officer and I received an order. If I could not carry it out, I would feel shame. I am very competitive,” he added.
While on Lubang Island, Hiroo Onoda surveyed military facilities and engaged in sporadic clashes with local residents.
Three other soldiers were with him at the end of the war. One emerged from the jungle in 1950 and the other two died, one in a 1972 clash with local troops.
Hiroo Onoda ignored several attempts to get him to surrender.
He later said that he dismissed search parties sent to him, and leaflets dropped by Japan, as ploys.
“The leaflets they dropped were filled with mistakes so I judged it was a plot by the Americans,” he told ABC.
Finally in March 1974 his former commanding officer travelled to the Philippines to rescind his original orders in person.
Hiroo Onoda saluted the Japanese flag and handed over his Samurai sword while still wearing a tattered army uniform.
The Philippine government granted him a pardon, although many in Lubang never forgave him for the 30 people he killed during his campaign on the island.
Following his surrender, Hiroo Onoda ran a ranch in Brazil, and opened a series of survival training schools in Japan.
Hiroo Onoda was one of the last Japanese soldiers to surrender at the end of World War II.
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