The Department for Education figures also reveal that the proportion of looked-after children and children in need who were persistently absent from school increased in 2017/18.
The average Attainment 8 score, which measures average achievement over eight GCSEs with extra weighting given to English and Maths, fell from 19.3 in 2017 to 18.8 in 2018, according to the figures.
This has seen the attainment gap between looked-after children and their peers widen slightly over the last two years, from a gap of 25.2 in 2017 to 25.6 in 2018 using this measure.
Despite the fall in the Attainment 8 score, the proportion of looked-after children to achieve a pass in GCSE English and maths has risen slightly, from 17.4 per cent in 2017 to 17.5 per cent last year.
However, the proportion of children in need, who are on the edge of care and known to social workers, to achieve GCSE passes in both subjects has fallen over the same period, from 19.1 per cent 18.7 per cent.
In comparison, 59.4 per cent of children not in care gained GCSE English and maths passes last year.
Progress scores for looked-after children in primary schools in reading, maths and writing have improved between 2017 and 2018. But at GCSE level it has remained the same.
The figures also reveal that average grades for looked-after children improve the longer a child has been in care.
The proportion of children in need and those in care who are persistently absent from school has risen at a faster rate than among their peers over the last four years, according to the figures.
Between 2015 and 2018 the proportion of children in need who have missed more than 10 per cent of lessons rose from 28.2 per cent to 31.3 per cent.
Over the same period, the proportion of looked-after children who met the "persistent absentee" threshold, rose from nine per cent to 10.6 per cent.
The proportion of all children to miss one in 10 of their lessons only rose from 11 per cent to 11.2 per cent.
The government's definition of absenteeism, includes both authorised and unauthorised absences, including truancy.
A spokeswoman for the charity Become said the figures show how children in care can struggle in school due to placement instability.
"Today's figures demonstrate the huge impact that childhood adversity has on children's ability to learn at school," she said.
"Most children who are either classed as ‘in need' or have gone into care have experienced significant trauma, whether through abuse or neglect, bereavement, or other instability.
"The children in care that we speak to really want to do well at school. However, they face a lot of instability, such as frequent placement moves between different foster carers or children's homes."
She cites Children's Commissioner Stability Index figures, which show looked-after children are twice as likely as their classmates to change schools midway through a school year, "which has a huge impact on their ability to succeed academically".
Education Secretary Damian Hinds said: "Education is the key to unlocking potential, and we cannot ignore the stark reality of the poorer outcomes for children who face chaotic lives or have experienced trauma or adversity.
"Society shares responsibility for improving outcomes for vulnerable children. That is why we've provided practical advice to schools and social workers to adapt the way they support them, including having a consistent and trusted member of staff to talk to. We are also investing £84m to support families and help provide stability at home.
"School leaders, social workers and other professionals have been responding to our Children in Need review to go further in improving outcomes and help us identify the support needed for those who need it most."