The charities are also offering three smaller grants adding up to £500,000 in total. Each winning project will be independently evaluated.
The collaboration came about after Sir Tom Hunter, Scotland’s richest man, pledged £1m to the BBC Children in Need appeal.
Ewan Hunter, chief executive of the Hunter Foundation, said: “Every young person deserves the chance to shine. Hopefully, Positive Destinations can show there are ways of making that a reality on a small scale – which can be adopted on a larger scale in the future.”
For more information email Children in Need, with Positive Destinations in the subject line. Full details will be available from 1 February on the charity's website. The deadline for applications is 30 March.