A Pentagon spokesman said the missiles had been launched "potentially towards targets in Israel".
The USS Carney, a guided-missile destroyer, was operating in the northern Red Sea on Thursday.
The Pentagon also said US troops in Iraq and Syria had been attacked several times in recent days.
Washington is on alert for activity by Iran-backed groups as Israel continues to attack Hamas targets in Gaza.
The Pentagon's Brigadier General Patrick Ryder said three land attack cruise missiles and several drones fired from Yemen had been downed.
There were no injuries reported from the incident and a US official said the warship did not appear to be the target.
"We cannot say for certain what these missiles and drones were targeting, but they were launched from Yemen, heading north along the Red Sea, potentially towards targets in Israel," he told reporters.
Brig Ryder added that information about the nature of the activity was "still being processed" and the attack may "be ongoing".
"Our defensive response was one that we would have taken for any similar threat in the region where we're able to do so against our interest personnel and our partners," he said.
In Iraq, drones and rockets have been launched at several bases housing US and other international forces, the Pentagon said.
One of the attacks caused injuries to "a small number of troops".
Iraqi militant groups had warned the US against supporting Israeli actions against Hamas in Gaza.
On Wednesday, a drone hit US forces in Syria, causing minor injuries, and another drone was brought down.
"While I'm not going to forecast any potential responses to these attacks, I will say that we will take all necessary actions to defend U.S. and coalition forces against any threat," Brig Ryder said.
There are various US bases in the Middle East, with warships, troops and fighter aircraft.
In the past week the US has sent two aircraft carriers, about 2,000 marines and support ships to the Middle East.
There are "no plans or intentions" for their use, the White House says.
But it means that if required, the US military assets would be in place to protect national security interests.
Yemen's Houthi rebels, which the US says are responsible for these most recent attacks, are backed by Iran.
The Houthis have been locked in a prolonged civil war with Yemen's official government - backed by Saudi Arabia - since 2014.
The Pentagon's Gen Ryder said the US is still analysing the attacks in Yemen, Iraq and Syria.
"Our focus is going to be continuing to ensure we are deterring a potential broader regional conflict," he said, adding that there was currently no information showing a direct connection to the 7 October attacks by Hamas in Israel.
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