WHO has said the vaccinations would take place in Egypt, Iraq, Jordan, Lebanon, the West Bank and Gaza Strip, and Turkey.
Syrian refugees fleeing their country's conflict have taken shelter in surrounding states, particularly Lebanon, Jordan, Turkey and Iraq.
The vaccination campaign comes after the discovery of polio in Syria for the first time since 1999.
The statement said at least 17 children had been paralysed by polio, 15 of them in the eastern province of Deir Ezzor, large swathes of which are under rebel control.
The other two cases were recorded in Aleppo in the north, and in Douma, near the capital Damascus.
"Inside Syria, the campaign aims to reach 2.2 million children, including those who live in contested areas and those who were missed in an earlier campaign," the statement said.
But the organisations noted that many children in Syria remain inaccessible to the vaccination campaign because of the ongoing conflict.
"All Syrian children should be protected from disease," said Ala Alwan, WHO's regional director.
"We appeal to all parties of the conflict in Syria to cooperate and facilitate pauses in hostilities over the coming six months to allow vaccination campaigns to reach all children."
Health groups consider there to be a high risk of polio spreading in the region.
The strain of the disease detected in Syria is related to a strain that originated in Pakistan and has also been detected in sewage samples in Egypt, Israel and the West Bank and Gaza Strip.
Israel itself has launched an emergency innoculation campaign.