The agreement — for which financial terms were not made available — gives RIM access to the latest Extended File Allocation Table technology, which makes the handling of large files easier.
Shares in RIM gained 2.4 per cent on the Toronto Stock Exchange following the annoucement, closing up 17 cents to $7.24.
As consumers use their smartphones for more and more multimedia applications such as watching and shooting high-definition videos, file sizes are ever growing.
Microsoft says the new system expands the size of files that flash memory devices can handle and increases the speed with which those files can be accessed.
"Today's smartphones and tablets require the capacity to display richer images and data than traditional cellular phones," said David Kaefer, general manager of intellectual property licensing at Microsoft.
"This agreement with RIM highlights how a modern file system, such as exFAT can help directly address the specific needs of customers in the mobile industry."
The deal comes as RIM works to launch the next generation of its BlackBerry smartphones.
The company's future is riding on the success of its BlackBerry 10 operating system and new phones expected early next year.
The new BlackBerry devices will arrive in a market already crowded with new offerings, including new smartphones from Nokia and Microsoft and several months behind the latest incarnation of the iPhone, which launches this Friday.
New smartphone sales numbers released Tuesday by research firm IDC show BlackBerry lagging far behind Android and Apple devices in global second-quarter sales.
Android and Apple dominated in smartphones, with 85 per cent of the worldwide market combined in the quarter.
Blackberry devices, meanwhile, came a distant third with 4.8 per cent of the market, compared to 11.5 per cent a year earlier.