The Lions narrowly avoided relegation to League One this season, finishing two points clear of the relegation places in the Championship while also enjoyed a run to the semi-final of the FA Cup.
The 51-year-old former Swansea City boss took charge of Millwall in November 2007 and feels that it is now time for him to pursue a new challenge.
|FOOTBALL LEAGUE LATEST
|13/8||Kenny Jackett is 13/8 with PaddyPower to be the next Wolves manager
Jackett led the south London outfit out of League One in 2010 and had been the longest-serving manager in the Championship and the sixth longest-serving in the entire Football League.
He resignation was reluctantly accepted by the Lions, with chairman John Berylson stating: "On behalf of the board, I want to express my thanks to Kenny for his fantastic service and achievements over the past five-and-a-half years.
"He has played a major role in creating a stable environment at Millwall which hadn't been the case prior to his arrival.
"On a personal level, whilst respecting Kenny's decision, I wish I could have persuaded him to change his mind. He was my first acquisition as chairman of the club and has proved himself to be one of the best. I am losing a great manager but he will remain a good friend and, hopefully, golf partner.
"We are now determined to move the club forward and build on the foundations Kenny has provided towards even greater success."