The Australian will undertake four tests at Motegi for Honda's R&D team, with the aim of evolving the RC213V and developing the new production-based racer Honda will sell to selected teams for next year's championship.
Honda however categorically ruled out Stoner making a race return.
A wildcard appearance at the end of the season, either in Japan or at his home Phillip Island event - where Stoner is undefeated for the past six years - had been the subject of speculation, but Honda insisted it is "now out of the question".
Stoner denied he had any urge to return to grand prix racing, saying the test simply sprang from his desire to ride a MotoGP bike again.
"It's been almost seven months now since [his final race at] Valencia and I'm still happy and comfortable with the decision I made to stop racing," Stoner said.
"Sometimes I miss riding my RCV, so I am happy that HRC asked me to do some tests in Motegi this year.
"This will allow me to enjoy what I miss: riding a MotoGP bike.
"I'm looking forward to getting on the bike and see how it has changed from last year and I'd like to thank Honda for this opportunity."
Stoner's life after MotoGP
Shuhei Nakamoto, HRC executive vice president, said he was looking forward to receiving Stoner's feedback following his testing programme.
"We are very pleased to have Casey back on a Honda," he said.
"He knows this machine very well and I'm sure he can help our engineers and technicians with the development of the RC213V.
"We will also ask him to test the new production racer and give us his initial feedback to assist us in producing the best machine possible."
Stoner scored 15 wins, 26 podiums and 17 pole positions during his two seasons with Honda, winning the 2011 world championship in the process.
He grew disillusioned with the sport however and, at the age of 27, opted to walk away. He subsequently switched to four wheels, joining the V8 Supercars Development Series. He will fit the four MotoGP tests around his V8s schedule.
Stoner told AUTOSPORT last month that he could not envisage rediscovering the urge to compete again in MotoGP.