In 2012, Stoner unexpectedly announced his retirement from MotoGP at the age of 27, surprising fans and competitors alike.
The Australian has since been part of Honda’s test roster and was testing the CBR1000RR at Suzuka in January.
"After riding the bike in Sepang a few months ago, I've been speaking closely with Honda about the possibility to take part in Suzuka," said Stoner.
"It's always been an event I wanted to do and something I was never able to consider when I was racing in MotoGP, due to our busy schedules.
"The bike is very different to a MotoGP machine, but it will be a new challenge and a chance for me to try something new and unlike what I've been used to in my racing to this point.
"I've been impressed with Michael van der Mark this season and Takumi Takahashi has a lot of experience on this machine, so I'm looking forward to hearing their comments and working together with them in preparation for the July race.
"Now I need to concentrate on my training to be ready for the race," he added.