With one year remaining on his contract, Bernier was traded by the Maple Leafs to the Anaheim Ducks in exchange for a conditional pick in the 2017 NHL Entry Draft on July 8, 2016 (the conditions were not met). Reunited with Ducks Head Coach Randy Carlyle, who had been Bernier's coach in the early part of his time with the Maple Leafs, he assumed the backup goaltender duties behind John Gibson for the 2016–17 season. Bernier made his Ducks debut in a 3-2 defeat to the reigning champions, the Pittsburgh Penguins, on October 15, 2016. He collected his first win with the Ducks in a 4-1 result over the Calgary Flames on November 6, 2016.