Mr Williamson also said ministers were looking at expanding “bubbles” of children in the classroom from the current maximum of 15 “to include the whole class”.
Schools closed to everyone except vulnerable children and those with a parent identified as a key worker on 20 March, in response to the coronavirus pandemic.
As the lockdown measures started easing at the beginning of this month, children in nursery, reception, Year 1 and Year 6 were encouraged to returning to primary schools in England, albeit in smaller class sizes.
Some Year 10 and 12 pupils – selected because they are sitting GCSEs and A-levels respectively next summer – returned to secondary schools and colleges this week.
Ministers now want all pupils in England to return to classrooms full-time in the autumn, ending a near six-month absence for many pupils.
“School is vital to every one of our children, that is why we will bring all children, in all year groups, back to school in September,” Mr Williamson said.
The education secretary said he understood “there is anxiety still among parents” about their children going back to school.
But he added: “I want to assure you that the well-being of your children is the absolute top priority for every single one of us.”
He said the government would publish guidance for schools within the next two weeks on how to bring children back “so that schools have the maximum amount of time to prepare for the next phase”.
It is a promise that many parents will have been waiting to hear.
Education Secretary Gavin Williamson has committed to all school pupils in all year groups going back full-time in September.
The part-time, online, often not-really-anytime lessons will be over.
But the much trickier question will be how to deliver this.
Even if social distancing is reduced – and class size “bubbles” of 15 pupils can be increased – there will still be massive logistical challenges.
Head teachers have warned any social distancing, even 1 metre, will require additional classrooms and teachers.
And they have been exasperated at time ticking away without any clear plan – with heads’ leader Geoff Barton complaining schools are working in an “information black hole”.
When the government had to U-turn on bringing back all primary pupils it was because nobody listened to similar warnings about lack of space.
But a September deadline is now in place – and there will be high political stakes if there is another failure to deliver.
Earlier, Prime Minister Boris Johnson said he was “determined to do everything” he could to get all children back in school from September.
“We will bring forward plans on how this will happen as soon as possible,” he said.
There are separate rules for managing the threat of coronavirus in England, Wales, Scotland and Northern Ireland.
Schools in Wales are reopening at the end of June, with only a third of pupils in class at any time, while in Scotland, schools are preparing to reopen on 11 August.