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.”
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.
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.”