The announcement came after a 2-1 victory over relegated Crewe Alexandra on the final day of the season.
Despite the triumph, his Imps side finished a disappointing campaign 12 points above the relegation zone in 17th.
Most Popular
-
1
What Michael Appleton said about potential Blackpool incomings as Charlton man is linked with a return
-
2
Michael Appleton provides Gary Madine injury update after Swansea City defeat
-
3
Michael Appleton's assessment of Blackpool's cruel late defeat to Swansea City
-
4
Late heartbreak for Blackpool as Jerry Yates misses penalty in cruel Swansea City defeat
-
5
Some good performances even in defeat: How Blackpool's players rated during Swansea City loss
Yet it has been a difficult season after narrowly missing out on Championship football last term, after losing 2-1 to Blackpool in the play-off final at Wembley.
Appleton spent over two-and-a-half years at Sincil Bank after replacing Danny Cowley in September 2019.
In total, he managed 142 games in all competitions, winning 58.
It's understood Appleton’s departure wasn’t entirely a surprise to the club, who have already drawn up a managerial shortlist.
It’s been mooted the former Manchester United youngster could be returning to West Brom as part of Steve Bruce’s backroom coaching staff.
In a statement, the 46-year-old failed to reveal the reason behind his departure but was full of compliments of his time in Lincolnshire.
“It has been a privilege to manage Lincoln City over the past three seasons,” Appleton said.
“While this season did not match the highs of the last, we have still had some memorable performances and results.
“Clive Nates (chairman) and the board, the players and all the staff throughout the club, have been fantastic colleagues over the past three years and I thank them all for their backing.
“I am sure they will continue to drive the club forward on and off the pitch with some really impressive foundations in place for the coming years.
“I would like to thank all of the supporters who have got behind me and the team. Lincoln City is a special club which will always be close to my heart.”
Nates, meanwhile, insisted there was no fallout.
"He leaves with our total respect, our best wishes and an open invitation to visit the LNER Stadium at any time in future,” he said in the club statement.
Appleton spent just two months as Blackpool manager during the 2012/13 season before moving on to Blackburn Rovers.
He has also managed Portsmouth and Oxford United, and was caretaker boss at West Bromwich Albion and Leicester City.
Last July, the 46-year-old revealed he required surgery having been being diagnosed with testicular cancer.
Appleton described the procedure as “a routine operation” to remove the tumour and spent a brief time out of the dugout during his recovery.