The 27-year-old Australian, world champion for Ducati in 2007 and Honda four years later, retired at the end of the 2012 season saying he was no longer enjoying racing.
Stoner said he was still happy with his decision to stop racing bikes and move into the second tier of Australian V8 car racing but had agreed to test for Honda at Motegi, starting on August 6 and 7.
"There are times when I miss riding my RC213V so I am really happy that Honda have asked me to do some testing in Motegi this year," Stoner told the Australian MotoGP website on Tuesday.
"It will allow me to enjoy what I miss which is riding a MotoGP bike."
Honda Racing told the website that there were no plans for Stoner to ride as a wildcard at any races this season, not even in his home race at Phillip Island in October.
"There have been rumours of a wild card races for Casey but this is out of the question," team principal Livio Suppo said.