The strike was in retaliation to a Houthi missile attack, which missed a US Navy destroyer, the second such attempt in four days.
The US Navy fired cruise missiles on Thursday, targeting three radar sites controlled by Houthi rebels in Yemen, the first direct US strike against the group, the Pentagon said.
The US strikes came hours after a missile fired from Yemen's Red Sea coast missed a US Navy destroyer, the USS Mason, in the second such attempt in four days.
Authorized by President Barack Obama, the strikes were conducted with Tomahawk cruise missiles fired by the destroyer USS Nitze, a US official said.
"Initial assessments show the sites were destroyed," Pentagon Press Secretary Peter Cook said in a statement.
The strikes "targeted radar sites involved in the recent missile launches threatening USS Mason and other vessels operating in international waters in the Red Sea and the Bab al-Mandeb," he said.
"These limited self-defense strikes were conducted to protect our personnel, our ships, and our freedom of navigation in this important maritime passageway."
The missile, meant for the USS Mason, was fired from rebel-held territory and crashed into the ocean before reaching its target.
The Mason and the USS Ponce, an amphibious transport ship, were previously targeted on Sunday by two missiles that also missed the target.
The Pentagon said, at the time, it would respond "at the appropriate time and in the appropriate manner."
The US, a longtime ally of Saudi Arabia, has provided aerial refueling of jets from a Saudi-led coalition striking Yemen and it supplies US weapons sales to the kingdom.
Michael Knights, an expert on Yemen's conflict at the Washington Institute for Near East Policy, said the missile attacks appeared to be the Houthis' response to an attack last weekend, widely blamed on Saudi-led forces, on mourners gathered in Yemen's Houthi-held capital Sanaa.
The White House says it is reviewing its support for Saudi-led forces in Yemen in the wake of Saturday's strike, which killed at least 140 people by one count.
Houthis reiterate denial
Yemen's dominant Houthi movement on Thursday reiterated their denial that they carried out failed missile attacks on the US navy destroyer, said the Saba news agency, citing what it called a military source.
"These allegations are unfounded and the people's committees have nothing to do with this action," the source told Saba, referring to the Houthi administration.
The Houthis are battling the internationally-recognised government of Yemeni President Abd Rabbu Mansour al-Hadi.
The Houthis, who are allied to Hadi's predecessor Ali Abdullah Saleh and are backed by Iran, have the support of many army units and control most of northern Yemen, including capital Sanaa.
Although the US has provided limited support for the Saudi-led coalition battling the Houthis, it also has focused its direct military role in Yemen to the fight against Al Qaeda in the Arabian Peninsula.
That general US policy might still remain in place, even after the retaliatory strikes on Houthi targets.
Yemen's war has killed at least 10,000 people, displaced more than three million and brought parts of the country to the brink of starvation.