Sir Kevan Collins said some children were still facing time off school, while the adults around them were still feeling the effects on the pandemic.
During an event on Wednesday, Sir Kevan was asked what the last year and a half - which has seen huge disruption to children’s ordinary school and social life - means for the wellbeing of children.
“To be honest with you, I don’t think we know,” he replied.
Sir Kevan added: “There is a story for every child here. The story of Covid for children hasn’t yet been written.”
Experts have found tens of thousands more children have sought help for mental health problems since the start of the coronavirus pandemic.
As well as facing coronavirus restrictions over the past year in everyday life, such as socialising, most children stopped going into school during the lockdowns last spring and at the start of this year.
Students have also had to spend time off school when having to self-isolate - which amounted to hundreds of thousands of pupils every week in England towards the end of last year.
During the online event at the Festival of Education, Sir Kevan said the Covid pandemic continues to influence the lives of pupils and those around them.
“Some children are still facing absence from school, parents - teachers as well as parents - are still facing the consequences of Covid, and some children have suffered loss, as well as teachers,” he said.
He added: “I’m sure it’s quite profound and I don’t think we yet really understand what it means for, for example, a three year old to have had over a year not being with many other children.
“Equally for a 16 year old, not having time out with lots of other teenagers doing what you do and shouldn’t do at 15 together as you learn to tackle the world on your own terms as teenagers do and should.”
Experts and campaigners have called for children’s wellbeing and play to be central to catch-up plans following the disruption from the Covid pandemic.
Earlier this month, a union found the mental health of pupils was the “single biggest concern” of its staff working in education.
Back in May, the government announced millions of pounds would go towards improving mental health support in schools to tackle the impact of the coronavirus pandemic by upgrading support available in education.
The week before that, NHS England said it was expanding its support in schools, with mental health teams ready to support more than one million children in the country and plans to increase this figure to around three million by 2023.