The Lions were 11th in the Championship and had not won in their previous four games when Harris, who returned in February for a second stint in charge of the club, announced he would leave earlier in December.
Since then they impressively ended play-off chasing Blackburn Rovers’ six-game winning run before being defeated 2-1 by Norwich on Boxing Day.
Neil takes over a mid-table club that has won just once in their past nine Championship games.
Having overseen promotion to the Premier League through the play-offs with Norwich almost 10 years ago, he left the Canaries in March 2017 after they returned to the second tier.
Later that year he took over at Preston, where he spent four years, before being sacked with the club 16th in the Championship at the time.
He joined the Black Cats on a short-term contract in 2022 and won promotion from League One through the play-offs shortly after, but left to join Stoke early the following season.
He has been out of management for over a year since his 16-month stay at Stoke came to an end in early December 2023, with the Potters 20th in the table.
Martin Canning, who worked alongside Neil at Stoke and Sunderland, has also moved to south-east London as assistant head coach.
Neil has likened the challenge he has at Millwall to the job he first took on at Deepdale in the summer of 2017.
“The opportunity was a great one for me,” Neil said on his arrival at Millwall.
“I think it’s very much similar to when I went in at Preston, going into a good environment.
“It’s not as if there are huge problems. The team wasn’t struggling and I had to go in and develop a style of play, maybe bring some of the younger players through, so I see this as a very similar project to what I did there.”