Stokes is currently banned from representing England while police investigate the street brawl he was involved in last month in Bristol.
Bairstow, who normally bats behind Stokes at number seven, said: “I batted at five earlier on this summer in Tests so it’s not something that would faze me too much because that’s something I’ve done for Yorkshire since I came into the side.
“Wherever (captain) Joe (Root) and (coach) Trev (Bayliss) want me to bat, that can only be a good thing for the side. As long as I’m in the side then I’m not too fussed.”
England would have been underdogs against Australia even with talisman Stokes.
Bairstow was part of the last England side to travel Down Under four years ago, when the tourists suffered a chastening 5-0 series loss.
But the 28-year-old insisted England must remain optimistic.
“It’s going to be a fantastic series,” he said. “It’s something that if you don’t look forward to it and you’re not excited about it then you’ve already lost the battle.
“It’s an exciting time; everyone speaks about it, not just in England, not just in Australia but all around the world.
“We know that we’re not just playing against 11 guys on the field, we’re playing against a whole nation, but at the same time if you play well you earn the respect of that nation. We know how good a place it is to tour.”
England fly to Australia on October 28, with the first Test starting in Brisbane on November 23.