As part of the Big Lottery Fund's HeadStart programme, the money will be divided between Blackpool Council (£10m), Cornwall County Council (£8.9m), Hull City Council (£7.8m), Kent County Council (£10m), Newham Council (£9.8m) and Wolverhampton City Council (£8.9m).
Councils will use the funding to work with young people, charities, health commissioners, parents, teachers, and GPs, to develop support systems for 10- to 16-year-olds.
Initiatives set to be offered include mental health "first aid" training; peer mentoring; advice on staying safe online; work to tackle social media bullying; and "resilience lessons".
Targeted support will also be provided to vulnerable groups and pupils displaying risk factors.
It is hoped the work will lead to shared learning and better evidence on what works to support effective prevention and early intervention.
Lyn Cole, Big Lottery Fund England grant-making director, said: "HeadStart has been developed with young people to ensure that mental health is embedded in a school's culture and pupils, emotional welfare is recognised as fundamental to their overall achievement."
"This will raise awareness, tackle stigma and enable young people to seek the support they need when they have problems and are under stress. This funding will make a huge difference to the development of young people at a crucial time in their lives."