It has set up the new model following discussions with the national schools' IT body Becta, which said it could provide schools with more flexibility in their use of software.
It will remove the requirement for schools using a Microsoft subscription licensing agreement to license the software giant's products across their entire ICT estate.
Becta said it should make it easier for schools that use open source software, such as Linux of OpenOffice, to mix these systems with proprietary software. This should give them scope to reduce their licence fee and save money.
The new agreement will also automatically give teachers, governors and other school staff a licence to use Microsoft products at home, as well as on school premises, provided they are using school laptops and PCs.
Becta said the pilot, known as Subscription Enrolment Schools Pilot, will initially only be available through the Microsoft's Education Large Account Reseller partners. A number of these resellers are available through a Buying Solutions education framework contract.
Stephen Crowne, chief executive of Becta, said: "The new flexibility will facilitate greater competition and choice in the marketplace and provides schools who wish to use Microsoft software with improved opportunities to achieve greater value for money.
"It will be important that schools and local authorities who wish to use Microsoft software now review their perpetual or subscription licensing options in the light of this new flexibility."
Alan Mo, senior analyst at Kable, said: "By increasing choice and offering greater flexibility, Microsoft will enhance its brand in the UK education sector. Conversely, the freeing of shackles is likely to open up competition. They've been careful to say 'potential cost savings', as buying less may not necessarily mean less cost."
