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The seven-year old left Hakodate City Hospital with his parents on Tuesday afternoon, carrying a large card shaped like a baseball filled with messages from well-wishers.
The boy answered reporters' questions about his condition, saying "I am okay." He told them he is looking forward to going back to school and taking part in sports day.
Tanooka's parents bowed to the doctor and hospital staff before taking their son into a silver van and driving away.
He had taken shelter in a building at the base, after his father left him by the side of the road to punish him for being naughty during a family trip to the woods on May 28.
No charges against parents
Police in Japan's Hokkaido prefecture said they won't pursue criminal charges against Yamato's parents.
However, they've lodged a complaint against them with the Child Constitution Office in Hakodate City on suspicion of psychological abuse, Toshifumi Goto, a spokesman for the Hokkaido Prefectural Police, told CNN.
Yamato's father Takayuki expressed remorse after his son was found on Friday, following a six-day search that involved more than 200 rescue workers and members of the Japanese Self-Defense Forces.
Yamato had survived his ordeal by huddling in the military base and drinking water from a tap outside.
"I never thought the situation would develop in such a way. I thought it would be good for him, but it was too much," Takayuki Tanooka told a press conference.
After questioning the boy for an hour on Monday, Hokkaido police told Japanese news agency Kyodo that his story was consistent with his parents' version of events.
Dr. Yoshiyuki Sakai, the doctor who examined Yamato when he was found last Friday, said he appeared to be in good condition for someone who had spent so long without food.
Junko Ogura and Yoko Wakatsuki contributed to this report.