Dani Pedrosa's future at the team is in doubt, with the Spaniard having been forced to take time off due to an arm pump ailment while also failing in the minds of some to really hit the required heights since joining the team in 2006.
Should Honda part ways with Pedrosda, Doohan feels that Stoner, who retired from the sport at the end of the 2012 season, would be the ideal replacement – if he wants to return to the sport.
"If he does want to come back, maybe he's an option for them to replace Dani Pedrosa for next year," the Australian told AAP of Stoner. "This is just my opinion.
"For me, Stoner retired too young and for the wrong reasons and this is why he wants to come back.
"But it's yet to be seen if he can step up to the challenge to compete against these guys."
Stoner walked away from the sport in 2012 having claimed 38 MotoGP victories on his way to winning two world titles.