Mr Williamson, who is from Scarborough, tweeted: “It has been a privilege to serve as Education Secretary since 2019.
“Despite the challenges of the global pandemic, I’m particularly proud of the transformational reforms I’ve led in Post 16 education: in further education colleges, our skills agenda, apprenticeships and more.
“This programme will create better life opportunities for pupils and students for many years to come. I look forward to continuing to support the Prime Minster and the government.”
His message was suggestive that he was not being offered another role as a frontbencher, but there has been no confirmation of whether he would be moved to a different role.
The Yorkshire Post was the first newspaper to call for the resignation of the much-criticised Education Secretary in January.Mr Williamson has faced criticism over his handling of the awarding of A-Level and GCSE grades during the Covid crisis, and the approach to school closures.
He apologised last week after confusing England footballer Marcus Rashford with rugby star Maro Itoje, wrongly claiming he had met the former while in fact he had spoken over Zoom to the latter man.
Kate Green MP, Labour’s Shadow Education Secretary, said: "Gavin Williamson has failed children and young people, their parents and our hard working education staff throughout one of the most testing periods in our history.
"Two years of exams chaos and staff abandoned, unsupported and demoralised. That is Gavin Williamson's legacy.
"The Prime Minister has allowed this to happen, keeping a failing Education Secretary in post for months and refusing to fight for children's futures."
Confirmation that a reshuffle was being carried out came as Mr Johnson led Prime Minister’s Questions in the Commons.
“The PM will today conduct a reshuffle to put in place a strong and united team to build back better from the pandemic,” a No 10 source said.
“Yesterday, the PM set out his plan for managing Covid during the autumn and winter.
“But the Government must also redouble our efforts to deliver on the people’s priorities.
“The PM will be appointing ministers this afternoon with a focus on uniting and levelling up the whole country.”
Robert Buckland has also departed the role of Justice Secretary.
He said it had been an “honour” to serve in the Government for the last seven years, including the last two as Justice Secretary and Lord Chancellor.
“I am deeply proud of everything I have achieved. On to the next adventure,” he said.
The courts system has been under huge strain during the pandemic, but a specific reason for his departure was unclear.
Robert Jenrick has also left his Cabinet role. He said it had been a “huge privilege” to serve as Communities Secretary as he confirmed his exit, saying he will “continue to support the Prime Minister and the Government in every way I can”.