She called the US departure a loss for "the United Nations family" and for multilateralism, saying the USA and UNESCO matter to each other more than ever now to better fight "the rise of violent extremism and terrorism".
Until that time, the United States, which provides around $80 million to UNESCO annually, will remain a full member.
Washington said it would establish an "observer mission" to replace its representation at the agency. It cited USA belief in "the need for fundamental reform in the organization".
The organization has a long history of taking anti-Israel measures, and supporting resolutions against the Jewish state.
Israeli Prime Minister Benjamin Netanyahu - who is also Israel's foreign minister - gave instructions to "prepare for Israel's exit from UNESCO parallel with the US", Netanyahu's office said in a statement on Thursday.
The UN General Assembly President Miroslav Lajčák is also "concerned that the decision by the United States to withdraw could have adverse impacts upon the important work of UNESCO", according to a statement from his spokesperson.
He said: "Unesco has become a battlefield for Israel bashing and has disregarded its true role and objective".
"Today is a new day at the U.N., where there is price to pay for discrimination against Israel", Israel's Ambassador to the United Nations Danny Danon said.More news: Aarushi murder case: Grandfather reacts to verdict, says grateful to HC
The U.S. move underscores the scepticism expressed by President Donald Trump about the need for the U.S.to remain engaged in multi-lateral bodies.
In addition to anti-Israel bias, the department cited "the need for fundamental reform" and "mounting arrears" at the organization. It is also a member of the United Nations Development Group.
UNESCO is a body of the United Nations that promotes worldwide cooperation in education, science, culture and communication, though it is perhaps best known for its designation of "world heritage" sites - locations with particular cultural significance. "It's not just about money, it's promoting ideals that are vital to countries like the United States, such as education and culture", a UNESCO-based diplomat said.
The U.S.is pulling out of UNESCO.
But according to Nikki Haley, the USA ambassador to the United Nations, the Trump administration found it to be a step too far when the agency decided this summer to designate "the Old City of Hebron and the Tomb of the Patriarchs as part of Palestinian territory".
Following years of tension at UNESCO, which is in the process of electing a new director-general, US State Department spokeswoman Heather Nauert announced that Washington planned to withdraw.
The country plans to become "a non-member observer state in order to contribute USA views, perspectives and expertise on some of the important issues undertaken by the organization, including the protection of world heritage, advocating for press freedoms, and promoting scientific collaboration and education".