Up to 10,000 crossed at Peshkhabour on Saturday, bringing the total influx since Thursday to 20,000. The UN says the reasons are not fully clear.
The UN agencies, the Kurdish regional government and NGOs are struggling to cope, correspondents say.
It comes as UN chemical weapons inspectors arrived in Damascus on Sunday on a long-awaited mission called by Syrian government.
The team will visit three sites over two weeks, including the northern town of Khan al-Assal which is at the center of allegations of chemical weapons use.
The Syrian government has filed several reports to the United Nations on militants’ use of chemical weapons against civilians and Syrian soldiers.
The UN High Commissioner for Refugees (UNHCR) says this is one of the biggest single waves of refugees it has had to deal with since the insurgency began in March 2011.
There has been a sharp rise in clashes between Syrian Kurds and anti-Syria extremist militants.
The charity Save the Children has launched an emergency response to the mass arrival, distributing basic supplies to those waiting to be registered.
"This is an unprecedented influx of refugees, and the main concern is that so many of them are stuck out in the open at the border or in emergency reception areas with limited, if any, access to basic services," said Alan Paul, Save the Children's emergency team leader, who is in the area.
"The refugee response in Iraq is already thinly stretched, and close to half of the refugees are children who have experienced things no child should."
SHI/SHI