Secretary of Defense Lloyd Austin said the strikes were in response to recent attacks on US bases in Iraq and Syria by Iranian-backed militia groups.
The US strikes were “separate and distinct from the ongoing conflict between Israel and Hamas,” he said in a statement.
Iran did not immediately comment.
The strikes, carried out by a pair of F-16 US air force fighters, took place on Friday at around 04:30 local time (01:30 GMT) near Abu Kamal, a town on the border with Iraq.
It is not yet known if there were any casualties from the attacks.
“These precision self-defence strikes are a response to a series of ongoing and mostly unsuccessful attacks against US personnel in Iraq and Syria by Iranian-backed militia groups that began on October 17
US and coalition troops have been attacked at least 12 times in Iraq and four times in Syria since the conflict between Israel and Hamas began.
A total of 21 US military personnel have suffered minor injuries, according to the Pentagon.
American officials attribute the attacks to Iranian proxy groups operating in the region. Iran backs both Hamas, which controls Gaza, and Hezbollah, which operates in Lebanon, with arms as well as money.
“These Iranian-backed attacks against US forces are unacceptable and must stop,” Mr Austin said.
“If attacks by Iran’s proxies against US forces continue, we will not hesitate to take further necessary measures to protect our people.”
In normal times, these air strikes would not be that remarkable.
But with a war raging in the Gaza Strip and fears of an escalation into a regional conflict there is an underlying worry that Iran and its proxies could soon get involved in the fight between Israel and Hamas, sparking a wider and even more serious war.
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