Two US service members were lightly wounded in the operation but were safely evacuated from the scene, a defense official told CNN.
The raid targeted a compound that was being used by AQAP "as a headquarters, a place to meet and plan for external operations," according to US Navy Capt. Jeff Davis, a Pentagon spokesman. The mission was to "disrupt" operations in a known safe haven, though another US defense official could not point to a specific disrupted operation.
The al Qaeda fighters were "likely not expecting us" because of how deep in Yemeni territory the raid occurred, Davis said. This was the "deepest we've ever gone into Yemen to fight AQAP," he said.
However, US forces were forced to call in an AC-130 gunship for air support when a firefight began, according to Davis. Additional fighters may have been killed by the strikes from the aircraft but Davis told reporters that there are "no credible indications of civilian casualties."
The raid was carried out with the support of the Yemeni government, according to CENTCOM.
"Raids such as this provide insight into AQAP's disposition, capabilities and intentions, which will allow us to continue to pursue, disrupt, and degrade AQAP," according to a press release by CENTCOM.
US special operations forces have stepped up ground operations inside Yemen in recent months amid growing concern that AQAP continues to plan attacks on Western targets, including commercial aviation.
The covert ground missions had previously been described as efforts to collect intelligence on the al Qaeda affiliate, including its top operatives and locations where its members could be hiding.
Tuesday's raid is the first ground operation acknowledged by the US since a Navy SEAL mission earlier this year resulted in the deaths of Chief Petty Officer William "Ryan" Owens and reportedly several civilians.
The Pentagon did not respond to questions from CNN as to why they decided to go public with the raid, but several defense officials said the Pentagon is under pressure from the White House to show progress on terrorism.
The US has conducted more than 80 airstrikes against AQAP in Yemen since February.