The all-rounder was given the nod ahead of opening batsman Andrew Strauss who has captained the side in the absence of the injured Flintoff during the recent Test and One-day series against Pakistan.
Flintoff, who succeeded the injured Michael Vaughan as England skipper, has not played for his country since the drawn series against Sri Lanka because of an ankle injury although he expects to be fit for the first test in Brisbane on Nov. 23.
Left-arm spinner Ashley Giles, one of the key figures in England's Ashes triumph last year, was also named in the squad despite missing the entire season with a hip injury.
As expected, there was no place for Vaughan, who is still battling to recover from a right knee injury, although he has not ruled out playing some part in the tour.
Chairman of selectors David Graveney said choosing between Flintoff and Strauss had been a difficult task.
''We have had to make a very tough decision in choosing between Andrew Flintoff and Andrew Strauss for the captaincy and we were fortunate to have two such outstanding candidates available to us in Michael Vaughan's absence,'' Graveney told the ECB Web site.
''Ultimately, we took the view that Andrew Flintoff had demonstrated excellent leadership skills during a difficult tour of India earlier this year, that he was the man in possession and deserved a further opportunity to continue as captain.'' Giles will continue his rehabilitation from injury by travelling with the One-day squad to the Champions Trophy in India next month, although he will not be eligible to play.
There are also fitness worries over bowlers Stephen Harmison and James Anderson, although both are expected to play first-class cricket before the end of the domestic season.
Squad: Andrew Flintoff (captain), Marcus Trescothick, Andrew Strauss, Alastair Cook, Kevin Pietersen, Paul Collingwood, Ian Bell, Chris Read (wicketkeeper), Geraint Jones (wicketkeeper), Ashley Giles, Monty Panesar, Stephen Harmison, Matthew Hoggard, Sajid Mahmood, Liam Plunkett, James Anderson.