The daylong naval bombardment zeroed in on targets located near Zinjibar in the southern province of Abyan, according to reports by The Associated Press.
American unmanned drones reportedly took out 25 al Qaeda fighters during March 10 raid in the southern Yemen town of Bayda, southeast of the country's capitol Sanaa, Reuters reported at the time.
The Pentagon confirmed that U.S. fighters also hit Abyan in a second round of airstrikes a day after the Bayda raids, targeting suspected militants in the province.
The naval strikes come less than a week after Ansar al-Shariah, a jihadist group tied to the AQAP claimed to have shot and killed American Joel Wesley.
Wesley was working as a teacher at a language institute in the southeast city of Taiz when he was killed.
Taiz is the second largest city in Yemen and was a center of the anti-government protests that ultimately ousted longtime Yemeni leader Ali Abdullah Saleh from power in February.
Two members of the radical Islamist group, disguised as Yemeni soldiers, allegedly shot Wesley as he sat in his car on March 11, according to news reports.
The terror cell branded Wesley, who arrived in Yemen in 2010, an "enemy of Islam" for preaching Christianity to locals during his tenure at the institute, the report states.
The killing is the latest in a string of attacks carried out by Yemen-based terror groups.
Islamic militants kidnapped and killed a senior Yemeni security officer in the southeast Hadramout province a day before the Navy bombardment of Zinjibar.
The body of Lt. Col. Farag Said Ben Qahtan was found in farmlands following a gun battle between the kidnappers and security forces trying to rescue him, according to the AP.
Pentagon and intelligence officials have recognized al Qaeda's Yemen cell as one of the group's most active and dangerous.
AQAP leaders were behind a failed 2009 plot to blow up an American airliner above Detroit and a 2010 attempt to set off a car bomb in the middle of Times Square in New York City.
Former AQAP leader Anwar al Awlaki is believed to have spurred on Nidal Malik Hassan to kill 13 U.S. soldiers during a shooting spree at the Army's base in Ft. Hood, Texas.
The American-born Awlaki was killed in an air strike by a U.S. unmanned drone last September.
It was the first time the White House approved the targeting and killing of a U.S citizen in a counterterrorism operation.