The airbridge, using Ilyushin-76 commercial cargo planes to Hassakeh from Arbil, northern Iraq, will begin tomorrow.
Up to 12 flights are scheduled until Sunday, said Amin Awad, director of the agency's Middle East and North Africa Bureau.
UN agencies have ferried limited aid supplies into Syria from Iraq and Lebanon, but not via Turkey because of objections from Syrian President Bashar al-Assad's government. Mr Awad said: "This is the first time the aid goes through Iraq."
The cities of Hassakeh and Qamishli, where there are 60,000 vulnerable people, will receive food and relief items. The cargo will include blankets, kitchen sets, plastic tarpaulins for shelter, sleeping mats, and jerry cans.