A YJB report on action taken and lessons learned in relation to deaths in youth custody since 2000 found that of the 16 under-18s who have died, at least 11 were in care at some point.
The report highlights a number of steps taken by the YJB to improve support for looked-after children, including placing social workers in all young offender institutions, and reveals that a review of provision will be held this year.
YJB chief executive Lin Hinnigan said her organisation would also hold discussions with local authorities and the Department for Education on the issue.
"We are concerned about the over-representation of looked-after children in secure accommodation," she said.
"The fact that their needs are not being met in the care system is something we need to look at."
The report goes on to state that bullying also presents a "major challenge", and work is under way alongside secure estate providers to develop and share effective practice such as restorative justice to tackle bullying and violence.
"We want staff in secure establishments to better understand the causes and impact of bullying and to better address the needs of both victims and perpetrators," the report adds.
The YJB has also pledged to take action in three other areas: listening to children about what they need to keep safe; continuing to improve information sharing so young people are held in the most appropriate placement; and understanding better how to support children at risk of self-harm or suicide.
Publication of the report comes two weeks after Justice Secretary Chris Grayling announced that the government will hold an independent review into the self-inflicted deaths of 18- to 24-year-olds in custody.
Hinnigan told CYP Now that she is open-minded about the possibility of the review being extended to under-18s, but will not be taking a decision on whether to back calls for it to happen until the findings of investigations into two of the most recent deaths are made public.
She added that she believes youth custody is now safer than it was in 2000.
"I do think we have done a lot, specifically around placement and restraint where we have come a long way", she said.
"I think we have made big progress there and in other areas, but we are by no means complacent. We are constantly challenging ourselves to think about our safeguarding responsibilities."
She said that the organisation will focus over the coming years on how to ensure proposed secure colleges provide a safe environment for young people.
Youth justice experts have expressed safeguarding concerns about secure colleges, highlighting the dangers of holding 12- to 14-year-olds and 15- to 17-year olds boys on the same site, albeit in separate accommodation.
Speculation has also arisen that girls may be held in secure colleges as well, again, in separate accommodation.
"There is a lot of hypothesising," Hinnigan said. "Girls [being held in secure colleges] is something we are not yet sure on.
"There are many aspects we are not sure on until we get to the specification of the regime and rooms. There are people jumping to conclusions, which is unfortunate.
"The YJB is working closely with the Ministry of Justice (MoJ) to make sure that the design is such that children will be safer.
"It is too early to know what it will look like and whether they will be safer, but that is what the YJB is driving for."
Frances Crook, chief executive of the Howard League for Penal Reform, said that, while the report is welcome, she is disappointed that the deaths of under-18s in custody are not included in the scope of the independent review announced by the Ministry of Justice.
She added that an opportunity had been missed with the report.
"Through its youth offending teams, the YJB has responsibility for children when they first start to get into trouble, and its duties to care for their welfare must be paramount.
"The failure to consider what happens before they have entered custody and the sentencing decision is a serious mistake.
"This report focuses only on what happened to them after they were incarcerated."
Deborah Coles, co-director of the charity Inquest said:
"Whilst this report offers some insight into the YJB's learning from child deaths, it can be no substitute for a wider review.
"Inquest's work on the deaths of children shows the same issues of concern repeat themselves with depressing regularity. This demonstrates that the current mechanisms, including the YJB, are not preventing deaths of children.
Coles added that government proposals relating to restraint and secure colleges for children also call into question the extent of the impact the YJB's learning is having on policy-making.
"A short report cannot be a substitute for a full, holistic, independent review of child deaths in custody that encompasses all findings and recommendations, and examines the wider public health and welfare issues and a child's journey into the prison system," she said.
"The government must extend the remit of the inquiry it is commissioning into the deaths of 18-to 24-year-olds in prison to include children."