The clubs are intended to spark inspiration and to foster long-term interest in subjects such as physics.
Employers have been concerned at the shortage of science and technology skills among the workforce.
This pilot project will give after-school clubs £17,000 backing spread over two years - with the aim of reaching 5,000 pupils.
"After school science clubs like this will play an important role in helping to inspire our young people to be the scientists of tomorrow," said the Science Minister, Malcolm Wicks.
"We face important challenges today such as climate change and competing in the global environment. The importance of science and innovation to our economy and the wider world cannot be overestimated," said the minister.
There have been warnings from employers about skills shortages in the workforce – and some science departments in universities have struggled to recruit students.
And the Higher Education Minister, Bill Rammell, said it was "crucial that young people are inspired to study science at an early age.”
