The escalation in hostilities began with Monday's downing of a US Apache helicopter near the Strait of Hormuz, which sparked a series of tit-for-tat attacks across Iran and on US bases around the region.
It has been the most serious threat to a fragile ceasefire agreed in April, dampening hopes for a swift end to the war that started in late February with massive US-Israeli joint air strikes on Iran.
The US military said its latest attacks on Thursday targeted "military surveillance capabilities, communication systems, and air defence sites across Iran" in response to what it called Tehran's "unwarranted and continued aggression".
Trump told Fox News reporter Trey Yingst the US strikes would stop shortly but that he would resume heavy bombing if Iran's leaders did not sign an agreement with the US immediately, Yingst wrote on X.
The military's Central Command announced the strikes were complete about four hours after having begun soon after midnight in Tehran.
Iran's Islamic Revolutionary Guard Corps (IRGC) said it had launched counterattacks on 18 US military targets at air bases in Kuwait and Bahrain, as well as the US Navy's Fifth Fleet in Bahrain.
It later said it had also targeted the al-Azraq air base in Jordan for a second night running, firing 12 ballistic missiles at the US base.
Bahrain's interior ministry said an 11-year-old girl suffered minor injuries, while vehicles caught fire and homes were damaged in the town of Hamad and the capital, Manama, after debris fell from intercepted Iranian drones.
Kuwait said it briefly closed its airspace due to an Iranian attack.
Iran's military also warned it would fire on any vessel trying to pass through the Strait of Hormuz, which has been largely closed for months.
Iranian media said two US ships were fired on.
US Central Command denied the strait was closed or any of its ships struck, saying commercial ships were still transiting the strait despite Iran's threats.
The US has maintained its own blockade on Iranian ports and said on Wednesday it had fired on a vessel in the Gulf of Oman that flouted its instructions and was carrying oil from Iran.
India said three missing seafarers from the vessel had died.
Iranian news agencies reported explosions in several cities across the country, including Sirik, Kargan, Bandar Abbas, Minab, and Karaj.
US Defense Secretary Pete Hegseth presented the move as an effort to force Iran into a deal to end the conflict.
The strikes would "advance our military interests and also enhance our diplomatic position", he told reporters during a visit to Central Command in Florida.
"We will strike them hard tonight, and hopefully Iran makes a good decision," he said.
"If we need to negotiate with bombs, we'll negotiate with bombs."
The US and Iran have traded fire several times since the ceasefire took hold, even as negotiators have tried to end the war, now in its fourth month.
Trump has repeatedly said a deal is close, though there has been no sign of a breakthrough, while also threatening to resume bombing.
The war has killed thousands and disrupted roughly a fifth of global supply of crude oil and liquefied natural gas, sending prices sharply higher, and becoming a political headache for the White House before congressional elections in November.
Fighting continued in a parallel war in Lebanon between Israel and Iran-backed Hezbollah militants.
Israeli air strikes in southern Lebanon killed at least 13 people on Wednesday, Lebanese security sources said, while Hezbollah claimed fresh attacks against Israeli forces.
