The humanitarian group, also known as Médecins Sans Frontier, or MSF, said it had no other option.
The group blames the Saudi-led coalition force for carrying out "indiscriminate bombings," and it complains about "unreliable assurances" from the Saudi government, especially after the suspension of peace talks between the coalition and the Houthi forces in Kuwait earlier this month.
"Over the last eight months, MSF has met with high-ranking Saudi-led coalition officials on two occasions in Riyadh to secure humanitarian and medical assistance for Yemenis, as well as to seek assurances that attacks on hospitals would end," the organization said on its website.
It cites a recent incident on August 15, when 19 people were killed and 24 wounded after an airstrike hit a hospital in northern Yemen
"Aerial bombings have, however, continued, despite the fact that MSF has systematically shared the GPS coordinates of hospitals in which we work with the parties involved in the conflict. Coalition officials repeatedly state that they [honor] international humanitarian law, yet this attack shows a failure to control the use of force and to avoid attacks on hospitals full of patients. MSF is neither satisfied nor reassured by the Saudi-led coalition's statement that this attack was a mistake."
Earlier this year, at least 78 civilians were killed in March when Saudi airstrikes struck a market in northern Yemen.
Saudi's state run media reported that the coalition has set up an independent team to investigate reports of civilian casualties.
"We greatly value the work MSF does for the people of Yemen under difficult circumstances," reads the report from the Saudi Press Agency. "We are seeking urgent discussions with MSF to understand how we can work together to resolve this situation."
Yemen in many ways has become a proxy battleground for Saudi Arabia and Iran.
Yemen's minority Houthis, who are Shiite, rebelled last year against the Sunni-led government of President Abdu Rabu Mansour Hadi, backed by Saudi Arabia. That spurred the Saudi-led coalition to launch airstrikes in support of Hadi against rebel targets in Yemen In March of 2015.
Thousands of civilians have been killed in the violence. The United Nations estimates 9,000 casualties, including over 3,200 civilian deaths in the Yemeni conflict from March 2015 to March 2016.
Government forces and the Saudi-led coalition also have fought against the Al Qaeda branch in Yemen (AQAP) and ISIS, both of which are anti-government Sunni terror groups.
Doctors without Borders tweeted Thursday that it condemned "all involved actors - the Saudi-led coalition, the Houthi and their allies" because they "are conducting this war and carrying out indiscriminate attacks without any respect for civilians."
MSF will be evacuating its staff from four hospitals in Saada and two in Hajjah.