The money has come from Farnborough science and research organisation QinetiQ and will be used to fund the school's specialist science college application.
QinetiQ has offered the cash as part of its active sponsorship of local education schemes promoting science and technology.
As part of the sponsorship QinetiQ will also be talking to pupils about future careers in science and technology, as well as talking to them about the company's balloon mission this summer.
The ‘Science for Life' scheme is part of a new government initiative for improving education standards.
This gives Weydon School and many others the opportunity to become a centre of excellence in the specific subject area they have chosen.
The school has a series of projects within the community and the school, including the use of a fully equipped science bus.
A major part in the school's bid to become a specialist school is to raise £50,000 using independent funds.
Once the funds have been raised and it has passed a government inspection, it will be granted £600,000 over a period of four years, to be spent on its chosen subject.
Pictured from left with the £5,000 cheque are headteacher Lynne Jackson, Jasmine Ennor, deputy head Cathy Anwar, Alyson Coombes, Harry Sloan and Dr Dolores Byrne from QinetiQ.