The nine areas are: Brighton and Hove, Devon, Doncaster, the London Borough of Merton, North Yorkshire, North Tyneside, Salford, Staffordshire and West Berkshire.
Each will test the use of an assessment that is focused on building trust between the professional carrying out the test and the child, through the APP (attention, perspective taking and providing empathy) model.
The assessment will also include the views of those around the child, including their carer.
A common barrier with current testing that the pilot aims to address is a difficulty in engaging children in conversations about their emotional wellbeing.
A consortium led by the Anna Freud National Centre for Children and Families (AFNCCF) and including Action for Children, Child Outcomes Research Consortium and Research in Practice is running the pilot.
"A new assessment framework is to be introduced, with the child or young person at the heart of these assessments," said Sheila Redford, AFNCCF's head of service, specialist trauma and maltreatment.
"The approach will be more relational, include the young person's carer, and bring together views of those around the child.
"The aim is to increase awareness of the level of the young person's mental health needs and create a shared understanding of these needs across the important people in the child's network."
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The pilots will also be evaluated by research company SQW, which will look at the effectiveness of the assessments, ways they can be improved and sharing the results among other councils.
Research in Practice director Dez Holmes added: "The calibre of applications received showed local areas are making great strides towards improving the mental health assessments for children entering care through innovative practices, partnership working, as well as a strong operational and strategic commitment to improving the lives and outcomes of children and young people.
"Areas selected for this project demonstrated a high level of expertise and commitment to innovation."
"As the consortium starts working with the selected sites, we look forward to sharing the learning from the pilot with colleagues nationally."
Merton Council's cabinet member for children's services Kelly Braund said the pilot has the potential to "significantly" improve support for looked-after children.
"Nationally, too many children come into our care with mental health issues which have gone undiagnosed and better mental health assessments will ensure that we can provide support tailored to each child's needs," she said.
"There is a strong link between a child's mental and physical health, so improving their wellbeing can also benefit their overall health."
The pilot was due to start in May 2017 but was delayed due to the snap general election.
Bidding to take part launched in September last year.