The 2007 and 2011 World Champion has made occasional test appearances for Honda, since his retirement in 2012, at the end of the season.
The Motegi test ride on Thursday was the first time the Australian rode in almost a year. His main target was to continue working on the new bike.
Team Repsol Honda riders, Marc Marquez and Dani Pedrosa already tested the 2015 motorcycles last August but thought it was too early for them to decide.
Stoner admitted, saying, It took some time to get used to riding the bike again after a year off it."
"But everything felt good, I got back into the swing of things pretty quickly and we just got on with the testing programme HRC had planned.
"Day one went pretty well, testing both Marc and Dani's set-ups on the 2015 prototype machines and analysing these side by side we found some interesting differences and useful data.
"We also did some engine development and some other new items Honda brought for this test."
Factory MotoGP teams have already started testing the Michelin tyres, before they take over Bridgestone as control supplier for 2016. They are however, not allowed to use their team riders.
Honda though, called Stoner for the testing process and Yamaha will rely on their long time factory rider, Colin Edwards for the sessions.