In a statement, Samsung confirmed the acquisition of the Israeli company, with insiders tipping that the Korean company had paid around $30M for the business.
The Samsung statement said the aquisition will help the company to "continue to improve the overall user experience across our connected devices," it added.
Boxee's latest product lets subscribers record TV shows onto its servers, then stream them to TVs, computers and smart devices "from the cloud".
It had previously raised $26.5m and was set to do a further raising, prior to Samsung buying the company.
According to Informa Telecoms and Media, the takeover might prove a good match because, despite its apparent success, Samsung is still struggling to convince consumers to use its Smart TV services, rather than those of others.
Paul Jackson, principal analyst at Informa, told the BBC: "When people are going into stores, they may end up with a smart TV by default, but at the moment they have little desire to use their internet functions, even if they have a fast enough connection."
"But within the TV industry, there is a lot of optimism that consumers will want to use these kind services in the future.
"Boxee has been playing with its own TV user interface and has a good reputation for making a link between its hardware and a back-end service.
"But it's still early days for cloud TV services and it's been difficult for Boxee to make money. It makes more sense for it to be part of a wider offering, rather than selling itself as a single function device."