The 23-year-old, who won the all-around title in London earlier this month, said the teenager had chased after him on her bicycle.
"I was scared so I ran into the house and hid," Uchimura told Japanese media. "There's no doubt that was a stalker. I'm happy for the support," added the triple world champion.
"But if you come to my house I'm going to think you're a stalker.
Just three days ago, after an open-top bus parade for Japan's Olympic medallist attracted 500,000 people, Uchimura said he felt "like a celebrity".
Uchimura, already a household name in Japan, captured the Olympic title earlier this month after letting it slip through his fingers in Beijing four years ago.
After attending several official ceremonies and receiving more awards since returning from London, Uchimura had a favour to ask his growing fan base.
"I have to forget London and concentrate on what's next," he said, adding that he had taken to wearing sunglasses to disguise himself while riding his bicycle to training.
"I'm still pretty drained. I'd like the fans to just stick to (seeing me at) the venue."