Flannery, who joined TEN in January 2012, will depart on February 28.
The news will come as little surprise to industry observers, given former Seven exec, Peter Meakin, is about to begin as Executive Director of News and Current Affairs.
Meakin is due to start on February 17th.
TEN CEO Hamish McLennan, said: “I would like to thank Anthony for his hard work and contribution over the past two years.
“Our News operation has become stronger and more efficient over that time and our flagship TEN Eyewitness News bulletins at 5pm continue to dominate their timeslot in Sydney, Melbourne, Brisbane, Adelaide and Perth. We wish Anthony all the very best for the future.”
Flannery said: “TEN Eyewitness News is an outstanding operation with an exceptionally talented and committed team. I couldn’t be more confident about its future. I wish Hamish, Peter Meakin and all the great staff at TEN the very best.”