The support of 209 million euros will be used to help refugees stranded in the country rent homes and pay for basics with a cash card.
The move marks a change from previous projects which mainly provided support for accommodation in camps and the provision of direct supplies.
The scheme, announced with UNHCR, the U.N. refugee agency, will provide 22,000 rented homes in cities and towns on mainland Greece and some 2,000 places on the islands.
It will increase the number of refugees living in rented apartments in Greece up to 30,000 by the end of 2017, the Commission said.
“Our new funding is a game changer on how we deliver aid to improve people’s lives,” Christos Stylianides, the EU’s commissioner for humanitarian aid and crisis management, said in a statement.
“The aim of these new projects is to get refugees out of the camps and into everyday accommodation and help them have more secure and normal lives,” he said.
Part of the aid will go to providing refugees with a card with a set monthly cash allocation to help them pay for basic needs such as food, medicine and public transportation.
Thursday’s funding more than doubles the EU’s emergency support to Greece to a total of 401 million euros.
Currently, more than 62,000 refugees, mostly from Syria are stranded in Greece.