The general secretary of the Labour party, Iain McNicol, has stood down “to pursue new challenges” after serving for a “tumultuous seven years”.
In a statement, issued late on Friday, Mr McNicol said he would continue to work “in the service” of the party.
Labour leader Jeremy Corbyn thanked him for his service, adding he had been “a credit to our movement”.
The Conservatives said Mr McNicol had been toppled after “persistent attempts” by supporters of Mr Corbyn.
A spokesman said: “Iain McNicol’s departure shows once again that Labour are putting their own bitter internal politics before ordinary people and their priorities.”
Mr Corbyn praised the former trade union official’s long and dedicated service.
“He has run our party’s organisation at a time of great change, including a near tripling of the membership, two general elections and the EU referendum,” he said.
Mr McNicol said he would continue to support Mr Corbyn’s leadership and work closely with him.
‘Debt of gratitude’
The general secretary is the party’s most senior employee, responsible for employing staff, running campaigns and organising conferences.
He or she also acts as the non-voting secretary of Labour’s National Executive Committee – the governing body of the party.
A number of Labour MPs have paid tribute to Mr McNicol, with Chuka Umunna saying the party owed him “a huge debt of gratitude”.
Shadow Brexit secretary Keir Starmer said Mr McNicol had led his staff “with courage, conviction and dedication”.
Labour’s Stella Creasy said he left big shoes to fill with his “experience, passion and commitment” to the party.
Labour said officers of the party will meet to decide the process for the election of a successor.
BBC political correspondent Chris Mason said Mr McNicol’s resignation illustrated the changing of the political guard within the Labour Party.
He added that supporters of Mr Corbyn said Mr McNicol was “out of step with where the party now is”.
In 2016, the former general secretary publicly defended his staff when they were criticised by some of Mr Corbyn’s backers after he was re-elected as Labour leader.