Authorities in Blackpool, Kent and Newham in London have each been awarded £10 million to "spot the early signs", the Big Lottery Fund (BLF) said.
Council-led schemes in Cornwall and Wolverhampton were each granted nearly £9 million while £7.8 million will go towards a five-year project in Hull.
Lyn Cole, BLF grant-making director, said funds would "tackle stigma".
She said: "Mental health issues in early teens, if not tackled early, can develop into more serious conditions, impacting on school results and opportunities later on in life."
Phil Webster, who holds the portfolio for safeguarding children at Hull City Council, added: "Mental and emotional health is incredibly important in children's lives and we know from research that mental illness in young people often develops from age 14 onwards."
The six schemes were chosen from a pilot project, known as HeadStart, set up two years ago when 12 areas were awarded funding between £400,000 and £900,000 to develop long-term plans.
A BLF spokesman said the new grants would be used mainly for "providing a supportive school environment" through peer mentoring and tackling social media bullying.
"HeadStart will also provide targeted support to pupils showing risk factors such as repeated absences and disruptive behaviour," he added.
In 2014, the government announced it was investing £1.4 billion over five years in mental health services for children and young people.
Mental health projects in England will receive £55 million from lottery funds to support young people.