The announcement, which came at the Consumer Electronics Show (CES) in Las Vegas, is a big win for Microsoft, which is seeking to expand Windows 10 onto a wider variety of devices.
Samsung and Google, which makes Android, have an increasingly tense relationship as Samsung seeks more control over the software that runs on its phones. Partnering with Microsoft sidesteps these issues.
It's not immediately clear what devices Samsung is planning as part of the partnership. The South Korean company is known for its consumer appliances, such as smart fridges - so it could be that Windows 10 will make it way onto those.
"With Windows 10, both companies wanted to do something great together," said Terry Myerson, the head of Windows and Devices at Microsoft. The companies have a "shared vision for future innovation together across the entire Internet of Things," he said.
Microsoft has developed Windows 10 to work across a range of different devices and screen sizes, from the 84-inch Surface Hub to smaller IoT appliances, like a kettle. The company's stated aim is Windows 10 on one billion devices.