Stoner's first test will take place at Sepang from 29-31 January with a second session to be scheduled later in 2015. The testing will take place just days before the MotoGp season kicks off on 4 February.
The 29-year-old retired from racing in 2012, but says he is ready to get back on a bike for testing.
Stoner said:"After having a long break from riding, it was refreshing to get back on a bike a few months ago.
"Now after a relaxing Christmas and new year I'm happy to announce that I've been speaking to Nakamoto san and we have come to an agreement in continuing our relationship.
"I am currently preparing to ride in Sepang in a few weeks, which will be very different weather and humidity to Motegi, so I need to get myself fit!"
Nakamoto added: "We are very happy to be able to start 2015 by announcing the continuation of our relationship with Casey and keep him in the Honda family.
"The feedback he gives HRC is invaluable and we are fortunate to have a test rider capable to push the RC213V to its limits."