The Basic Skills Agency said the Pounds 1 million exercise in 103 schools had helped children who had lagged behind by between one and three years at primary school.
In order to qualify for a share of the Pounds 1m, schools had to say how they would boost basic skills.
During the 10-month programme most concentrated on literacy as the "gateway to the curriculum". Success was achieved using many methods though schools which saw the greatest improvement withdrew target pupils from lessons to give them extra help.
Continuous assessment was also used and literacy projects were integrated into many subject lessons. The children sat the same assessment tests at the beginning and end of the programme.
All but one of the secondary schools involved scored below the 1996 national average for five A-C grade GCSEs.
The agency intends to publish the results of the programme - its first major project in secondary schools - next month and to disseminate information about the most successful methods.
The agency's head of strategy Jim Pateman said: "The project gave us the chance to test 14,000 kids and look at what basic skills training works best at secondary level. These are catch-up programmes for kids who arrive at secondary school behind in their reading, and a lot of them have caught up quite considerably."