The Stabilisation and Association Agreement with the EU had originally been signed in Oct. 2015.
Speaking at a ceremony on Friday, Prime Minister Isa Mustafa said it was "an historic day for Kosovo".
The deal will help establish “a common market, regional cooperation and will also ensure the free movement of goods, services, labor and capital," Mustafa added.
Friday’s ceremony was attended by the EU delegation head to Kosovo, Samuel Zbogar plus the U.S. ambassador to Pristina Greg Delawie, among others.
The agreement consists of four main sections: political issues; harmonization of legislation; cooperation policy; and commercial issues. It will remain in force for 10 years.
Today’s deal is considered the first important step in Kosovo's EU integration process.