Mark Robins has resigned as Barnsley manager, three days after being placed on a 12-month notice period.
The 41-year-old, who joined the Tykes from Rotherham in 2009, had been considering his position after a disagreement over the club's budget.
"I'm disappointed that I'll no longer have the opportunity to continue the club's progress," said Robins in a League Managers Association statement.
The statement also stressed Robins had been working on a "limited budget".
On Saturday, Barnsley general manager Don Rowing told BBC Radio Sheffield there had been a disagreement over next season's budget.
But he said: "Mark has not been sacked. We would like him to stay and continue to develop the team for the future."
Rowing said the board had met with Robins during the week to discuss the Football League's proposals on the future of football finance, aimed at combatting high levels of debt and falling television revenues.
He said the Barnsley board had set their sights on breaking even and had discussed cutting the amount of money spent on loan players and reviewing their recruitment policy.
The club have also invoked a clause in Robins' contract, fixing the amount of compensation due if he was to leave, as well as placing him on a notice period.
Rowing said: "Mark will work his notice period until a year from now, when the notice was given.
"Mark wanted to look at his position. We were shocked that he took this stance because he is known for his fighting spirit.
"We expected him to take up the challenge - and it is a challenge that lies ahead of all football clubs. We all have to look to get our spending less than our income.
"I am confident Mark will be here for next season. He has a contract that states he will be here next year.
"As far as we are concerned we would like Mark to stay and continue to develop the team but that has to be Mark's decision.
"Hopefully he will come back next week and advise what he wants to do."
Robins guided Barnsley to 17th in the Championship this season, their highest finish for five years.
As a player, Robins had successful spells at Manchester United, Norwich City, Leicester City, Walsall and Rotherham.
He became assistant manager to Alan Knill at the Millers and replaced him as full-time boss in March 2007 following Knill's sacking.
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