The 26-year-old New Zealand international, who was born on Merseyside in England, was released by Port Vale in the summer having moved to Vale Park from the Iron in the January transfer window.
He has signed a two-year contract with Phoenix, claiming to have turned down several clubs in England.
The Phoenix chief executive Tony Pignata believes his experience in the English leagues will leave him in good stead for the season ahead.
"He's played in the Championship, which is an extremely good league," he said.
Mulligan joins Wellington Phoenix
"He offers us a lot of versatility given his ability to play at the back on the left or the right, as well as midfield.
"It just goes to show that instead of playing in the lower leagues in the UK you can have a great career in the A-League."
Mulligan joined Scunthorpe on a free transfer in the summer of 2006, playing in a total of 29 competitive games and scoring once.
Mulligan joined Scunthorpe on a free transfer in the summer of 2006, playing in a total of 29 competitive games and scoring once.
He spent two months on loan at Grimsby last season before making a permanent switch to Port Vale in January.