The U.N. High Commissioner for Refugees said the pontoon bridge over the Tigris River at Pashkhabour opened for passage this week, and was quickly put to use by thousands of Syrians crossing into Iraq.
U.N. observers said there was a surge of 5,000-7,000 people, many of whom had arrived at the border by bus, making the crossing.
The flow seemed to dwindle just as quickly, the high commission said.
"The factors allowing this sudden movement are not fully clear to us at this stage and as of (Friday) morning we are not seeing further large-scale crossings," UNHCR spokesman Adrian Edwards told reporters in Geneva, Switzerland.
The agency said many refugees told officials at the bridge they were on their way to stay with family members in northern Iraq, or were students studying in Iraq and had been home for the Eid holiday.
The British newspaper The Guardian said the U.N. and Iraqi authorities were waiting for the refugees and provided aid to help them on their way.
Ongoing violence in Syria has raised international concerns about Iraq's ability to handle a large influx of Syrian civilians.