Trump said a "full payload of BOMBS" was dropped on Fordo, in a surprise announcement that came just two days after he had apparently opened a two-week window for diplomacy.
He was set to address the nation at 10 pm (0200 GMT) after deciding to join Israel's strikes on Iran's nuclear program.
"We have completed our very successful attack on the three Nuclear sites in Iran, including Fordow, Natanz, and Esfahan," Trump said in a post on his Truth Social platform.
"A full payload of BOMBS was dropped on the primary site, Fordow."
Trump added that "all planes are safely on their way home. Congratulations to our great American Warriors."
In a second post announcing his address to the nation from the White House, Trump said that "IRAN MUST NOW AGREE TO END THIS WAR."
He also described it as a "historic" moment for the United States, Israel and the world.
Trump's shock announcement came just two days after he said he would decide "within two weeks" whether to join key ally Israel in attacking Iran.
Earlier on Saturday there were reports that US B-2 bombers -- which carry so-called "bunker buster" bombs -- were headed out of the United States.
Trump did not say what kind of US planes or munitions were involved.
- 'TIME FOR PEACE' -
Tehran had threatened reprisals on US forces in the Middle East if Trump attacked but the US president said that "NOW IS THE TIME FOR PEACE!"
Iran's President Masoud Pezeshkian had warned earlier Saturday of a "more devastating" retaliation should Israel's nine-day bombing campaign continue, saying the Islamic republic would not halt its nuclear program "under any circumstances."
Israel said on Saturday it had killed three more Iranian commanders in its unprecedented offensive, and Foreign Minister Gideon Saar claimed Tehran's alleged progress towards a nuclear weapon had been set back by two years.
Israel and Iran have traded wave after wave of devastating strikes since Israel launched its aerial campaign on June 13, saying Tehran was on the verge of developing a nuclear weapon.
On Saturday, Israel said it had attacked Iran's Isfahan nuclear site for a second time, with the UN nuclear watchdog reporting that a centrifuge manufacturing workshop had been hit.
Later Saturday Iran's Mehr news agency said Israel had launched strikes on the southern city of Shiraz, which hosts military bases.
And early Sunday, Iran's Revolutionary Guard announced that a "vast" wave of "suicide drones" had been launched against "strategic targets" across Israel.
Iran denies seeking an atomic bomb, and on Saturday Pezeshkian said its right to pursue a civilian nuclear program "cannot be taken away... by threats or war."
- 'Continued aggression' -
In a phone call with French President Emmanuel Macron, Pezeshkian said "we do not agree to reduce nuclear activities to zero under any circumstances," he added, according to Iran's official IRNA news agency.
Referring to the Israeli attacks, he said: "Our response to the continued aggression of the Zionist regime will be more devastating."
Iranian Foreign Minister Abbas Araghchi was in Istanbul on Saturday for a meeting of the Organisation of Islamic Cooperation to discuss the conflict.
Top diplomats from Britain, France and Germany had met Araghchi in Geneva on Friday and urged him to resume nuclear talks with the United States that had been derailed by the war.
Iran's Huthi allies in Yemen on Saturday threatened to resume their attacks on US vessels in the Red Sea if Washington joined the war, despite a recent ceasefire agreement.
The US-based Human Rights Activists News Agency said Friday that, based on its sources and media reports, at least 657 people had been killed in Iran, including 263 civilians.
Iran's health ministry on Saturday gave a toll of more than 400 people killed in the Israeli strikes.
Iran's retaliatory strikes have killed at least 25 people in Israel, according to official figures.
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