Their report, called 'Getting the house in order: Keeping homeless older teenagers safe', reveals 12,000 young people aged 16 and 17 go to their local authority each year for help because they have nowhere to live.
The charity said reasons a young person leaves home are often complex, citing the breakdown of relationships with their families and carers, or a need to escape domestic abuse or substance misuse.
Sam Reuston, Head of Policy at the Children's Society, believes some councils are taking the "cheaper option" of turning teens away
He told Premier: "It's shocking there are that many 16 and 17 year olds who are going to their councils asking for help with housing.
"But even more shocking is that almost half are being turned away without even a formal assessment being made - that puts them at real risk of either being returned to a home where they may be facing abuse or neglect, or even potentially physical violence, or may lead to them going missing or ending up moving from place to place."
"We need bed and breakfast use to be ended outright, and we need supported accommodation to be properly regulated so that children are put in places of safety."