The Lions were 11th in the Championship and winless in their previous four games when Harris, who returned for a second spell in charge of the club in February, announced he would be leaving at the start of December.
Since then they have ended the play-offs by chasing Blackburn Rovers’ six-game winning run before losing 2–1 to Norwich on Boxing Day.
Neil takes charge of a mid-table club who have won just once in their last nine Championship games.
He left the Canaries in March 2017 after they were relegated to the second tier, having overseen promotion to the Premier League via the play-offs with Norwich nearly 10 years ago.
Later that year he took over at Preston, where he spent four years, before being relegated with the club finishing 16th in the Championship at the time.
He joined the Black Cats on a short-term deal in 2022 and soon won promotion from League One via the play-offs, but left to join Stoke at the start of the following season.
He has been out of management for over a year since his 16-month stay at Stoke ended at the start of December 2023, with the Potters 20th in the table.
Martin Canning, who worked with Neill at Stoke and Sunderland, has moved to south-east London as assistant head coach.
Neil compared his challenge at Millwall to the first job he took at Deepdale in the summer of 2017.
“The opportunity was a great one for me,” said Neil on his arrival at Millwall.
“I think it’s a lot like going to Preston, going to a good environment.
“It’s not like there are huge problems. The team wasn’t fighting and I had to create a style of play, maybe bring in some young players, so I see it as a very similar project to what I’ve done there.”
