Mark Thompson has been on a fact-finding tour in the US
The non-exclusive memorandum of understanding sets out a framework for joint projects between the two organisations.
This includes plans for next-generation web 2.0 and ways to share online content in the future.
BBC director general Mark Thompson said there had been unprecedented rates of change in technology.
He said: "To ensure that the BBC is able to embrace the creative challenges of the digital future, we need to forge strategic partnerships with technology companies and distributors for the benefit of licence payers."
Mr Thompson and Ashley Highfield, director of new media and technology at the BBC, met Microsoft chairman Bill Gates on Wednesday as part of a fact-finding tour in Seattle, US.
They are also speaking to other companies, including Real Networks, IBM and the makers of the virtual world Second Life.
A BBC spokeswoman said the memorandum of understanding was the beginning of a dialogue between Microsoft and the BBC.
Potential areas of collaboration include search and navigation, distribution and "content enablement".
However, any procurement of new technology with the company would be subject to regulatory approval.
Bill Gates said: "Microsoft's strength is in driving digital innovation, and our vision is to open up rich, new consumer experiences that allow people to enjoy digital content anytime, anywhere and on any device.
"This vision fits squarely with the BBC's charter to lead the industry in delivering content that is compelling and accessible."