In a ratcheting up of the green agenda, she told a meeting of the Westminster Education Forum: "We have rethought our approach to sustainability. All new school buildings are required to be carbon neutral.
This is the first government programme where funding is dependent on carbon neutrality."
All secondary schools are due to be rebuilt or refurbished in the next 15 years under the Building Schools for the Future programme at an expected cost of pound;45 billion.
The carbon neutral rule will apply to new schools that have not yet been designed, but not to designs that have already received the government seal of approval.
Building work on the programme, which has been hit by delays, has now started in some areas. The first school is to open in Bristol in September.
Ms Brooks' comments built on an announcement made by Alan Johnson, the Education Secretary, that pound;110 million will be invested to deliver 200 low-carbon eco-schools over the next three years.
Mr Johnson said the experiment, which would promote designs with wind turbines, solar panels and low-energy lightbulbs, could lead to 2,000 carbon neutral schools and a reduction of 8 million tonnes of carbon dioxide.
Early experiments with low carbon schools have not proved successful. A number of designs ended up producing considerably higher levels of CO2 than had been expected.
With schools contributing around 15 per cent of the public sector's carbon footprint, the Government has been keen to make sustainability central to the BSF programme. But green tests for schools in the early wave of the project have been criticised for not being strict enough on carbon use.
New guidelines for school toilets were released this week to help tackle bullying. The guidance, to be used in all BSF schools, recommends making hand-washing areas more visible and placing toilet blocks opposite classrooms and staff areas so they can be supervised more easily. Unisex blocks are also recommended.