The cathedral was up against stiff competition from Stonehenge, Rutland Water and Tenby for the prestigious award.
More than 56,000 people took part in the vote for a winner.
Very Reverend Andrew Tremlett, Dean of Durham, told Premier: "We are thrilled with this; it's a fantastic award and an accolade for the cathedral."
The 11th century cathedral, which is part of the Durham UNESCO World Heritage Site, welcomes more than 750,000 visitors a year.
Rev Andrew said that it was easy to balance being both a popular visitors attraction and a place of worship.
He told Premier: "We love having visitors here. Lots of them will come because it's a beautiful building, world-class architecture with a Romanesque structure.
"But once they come inside the building, the prayers being said over a thousand years seep out through the stones and the stones start to say something back to them about the love of God."
Rev Andrew also said that a visit to Durham Cathedral was vital to understanding the history of the north-east.
"You can't understand the history of the north-east without understanding about the northern saints. St Cuthbert and Bede are buried here - it's a unique inheritance."
Previous winners of the Heritage Site of the Year title include: Hadrian's Wall, Severn Valley Railway and The Lost Gardens of Heligan.