The raid took place in Marib province in the early hours of today local time and was conducted with the support of Yemeni authorities.
Pentagon spokesman Navy Captain Jeff Davis said Al-Qaeda in the Arabian Peninsula (AQAP) fighters met the commandos with gunfire, and in the ensuing battle at least seven of the militants were killed.
The troops on the ground had to call in an AC-130 gunship for support, Davis said.
"This marks the deepest we have ever gone in Yemen to fight AQAP," Davis said, noting it was the first such operation since the ill-fated January 29 raid against AQAP that left multiple civilians and a US Navy SEAL dead.
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Davis said there were no "credible indications" of civilian casualties in today's assault.
Yemeni tribal sources said the operation targeted a residential block held by Al-Qaeda fighters in the village of Al-Hathla, in a mountainous district in the southeast of Marib province.
The dead were all members of the same Al-Aadhal tribe, the sources said.
The January raid was the first authorized by Trump, who drew criticism after he blamed "the generals" for having "lost" Navy SEAL Ryan Owens.
Washington regards AQAP to be the most dangerous branch of the extremist group.
A statement from US Central Command said the raid would "provide insight into AQAP's disposition, capabilities and intentions, which will allow us to continue to pursue, disrupt, and degrade AQAP."
America has supported the Saudi-led coalition through weapons sales, air-to-air refueling and some intelligence sharing.
The conflict has killed more than 8,000 people and wounded around 40,000, according to the World Health Organisation.
Seven ceasefires alongside UN-brokered peace efforts have so far failed to stop the fighting.