The "school performance index" awards were launched this week by the Curriculum and Assessment Authority for Wales (ACAC) with backing from the Midland Bank.
They will involve working out GCSE scores for every secondary school in Wales. Each school will be told its score in confidence and those which have improved most on an average over three years will be presented with framed certificates and special headed notepaper.
ACAC said the awards were intended to give schools an indication of how they are progressing and to supplement examination performance tables.
There will be local awards in the new unitary authorities and one or more nationally.
Midland Bank will provide framed certificates which will be given to the winners and headed notepaper for the scheme.
John Williams, ACAC chief executive, said: "This will give some formal recognition to those schools which have excelled."