The three-year contract extension will keep Emnes at Middlesbrough until the summer of 2015.
“We are delighted to have secured Marvin on a new, long-term contract,” said manager Tony Mowbray.
“After his successful loan spell with Swansea, Marvin came back into our team and made a huge impact towards the end of the season.
“He can be a big player for us again this year and it is a major boost for us that he wants to be part of our future and achieve his ambitions with Middlesbrough.”