The pilots will bring mental health experts into schools to identify problems with children and young people.
A spokesman for the Department for Children, Schools and Families said: "Early intervention in mainstream settings, in particular schools, is key to enabling children to learn, achieve and fulfil their potential."
Barbara Herts, departing chief executive of mental health charity YoungMinds, welcomed the move. "This is fantastically good news for mental health in schools," she said.
Herts added that there was scope for mental health work in schools to be linked to the Social and Emotional Aspects of Learning (SEAL) programme.
In July, Children's Secretary Ed Balls announced £60m over the next three years to fund the project.
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