Jayne Hrdlicka's appointment to the top job at Virgin Australia has raised doubts about its future, with unions concerned it means the relaunched airline will become a low-cost carrier as chief executive Paul Scurrah exits.

Ms Hrdlicka, a former Bain & Company consultant and ex-Jetstar boss, will take the reigns of Virgin 2.0 from early November. The announcement on Thursday put to end to months of speculation over what role she would play in the company after US private equity giant Bain Capital won a hard-fought bidding war for the nation's number two airline in late June.