In a series of tweets on Tuesday morning, Mr Trump accused Qatar of funding terrorism, saying: "During my recent trip to the Middle East I stated that there can no longer be funding of Radical Ideology".
The U.S. has a massive air base in Qatar's capital city of Doha, with hosts as many as 10,000 American military personnel.
The base is also the regional headquarters of United States special forces and Air Force commands - two vital components of American military operations in Afghanistan, Syria, Iraq and beyond.
Qatar's Emir Sheikh Tamim Bin Hamad Al-Thani and President Donald Trump meet at a hotel in Riyadh on May 21, 2017.
US President Donald Trump spoke to Saudi Arabia's King Salman and called for a united Gulf Cooperation Council to fight terrorism and promote stability in the region, amid deepening diplomatic crisis in Qatar.
"They said they would take a hard line on funding. extremism, and all reference was pointing to Qatar".
Qatar is far from the first casualty in the ongoing regional turmoil in the Middle East. Syria, Iraq, Yemen and Libya have become literal war zones in this battle for regional dominance.
The Pentagon cited no immediate effects from the instability on its operations.
"At that time, he was very heartened by the Emir's commitment to formally join the terrorist financing targeting centre and showing their commitment to this issue", he said.
Among diplomats and former USA officials there was shock that Trump would so openly pick sides in what is effectively a dispute between allies. The official reason given for the severing of ties was Qatar's alleged support for militant groups, including the Islamic State and (for Egypt) the Muslim Brotherhood. And it shouldn't be forgotten 15 of the 19 hijackers involved in 9/11 were also Saudi. Like earlier administrations, Trump's had kept its concerns private while publicly praising Qatari efforts to stamp out terror financing.
Sen. Bob Corker of Tennessee, the Republican chairman of the Foreign Relations Committee, says he wasn't aware of Trump remarks about Qatar and appeared surprised when reporters described what the president had tweeted.
Corker said: "We know that our Arab friends have differences, right?"
She could not say whether Trump was aware of the preparation to sever ties during his visit to Saudi Arabia. In backing the Saudis, the president offered unconditional support for a country that has fostered the spread of Islamist extremism across the world and that has supplied numerous foot soldiers for the Islamic State and al-Qaeda - not to mention most of the 9/11 hijackers.
USA officials were blindsided by Saudi Arabia's decision to sever diplomatic ties with Qatar in a coordinated move with Egypt, Bahrain and the United Arab Emirates (UAE), current and former officials in Washington told Reuters.
Qatar-based broadcaster Al-Jazeera said Tuesday Saudi Arabia's decision to shut its office in the kingdom as part of the diplomatic crisis in the Gulf was "unjustified".
"The Muslim Brotherhood denounces, with deep indignation, the accusations leveled against the group by Saudi officials", the Brotherhood said in a Wednesday statement.