The joint health and education department scheme was launched this week by Tessa Jowell, minister for public health, and education minister Estelle Morris.
The money will fund a pilot project in each of the eight health regions in England and Wales.
A government spokesman said: "The project should boost children's self-respect and self-confidence as well as their physical well-being."
The scheme will include a new Investors in Health award under which schools can measure themselves against national standards.
The launch took place at Deptford Green School in Lewisham, a London borough that already has its own healthy schools policy. Lewisham says that its programme has helped reduce exclusions, violence and bullying among pupils and has improved attendance.