One operation was carried out Saturday in Libya, where the US forces nabbed Al Qaeda leader Abu Anas al Libi, who was wanted in the 1998 bombings at US embassies in Kenya and Tanzania, reported CNN.
The second raid took place in Somalia, where US Navy Seals targeted a top leader of Al Shabaab, the militant group behind last month's mall attack in the Kenyan capital of Nairobi.
Pentagon spokesman George Little said in a statement that he can confirm that US military personnel were involved in the overnight operation against an Al Shabaab terrorist Friday, reported Xinhua.
He did not reveal further details, including the name of the targeted terrorist.
US Secretary of State John Kerry said the raids would make clear that the US "will never stop in its effort to hold those accountable who conduct acts of terror", the CNN report said.
"Those members of Al Qaeda and other terrorist organisations literally can run but they can't hide," Kerry said at the Asia-Pacific Economic Cooperation (APEC) summit in Bali, Indonesia.
Libi, 49, was on the FBI's "Most Wanted Terrorists" list with a $5 million bounty.
The Al Qaeda leader allegedly played an important role in the bombings at the US embassies in Kenya and Tanzania, in which at least 200 people were killed and over 1,000 injured.
The operation was conducted with the knowledge of the Libyan government and Libi was captured in broad daylight, CNN quoted an US official as saying.
Libi "is currently lawfully detained by the US military in a secure location outside of Libya", the Pentagon said.
No further details were disclosed.
In Somalia, a team of US Navy Seals took part in the operation against Al Shabaab, reported CNN citing a senior US official.
The Navy Seals came under fire and had to withdraw before they could confirm whether they had eliminated the target, the official said.
No US personnel was killed or injured in the operation, the official added.
An Al Shabaab spokesman was quoted by CNN as saying that at least one Al Shabaab fighter was killed in the gunfight.
Somalia state radio and local residents said Saturday that unidentified foreign forces attacked a house in the Al Shabaab-controlled southern Somalia town of Barawe in an overnight raid, reported Xinhua.
The attack was launched from the sea at a house protected by Al Shabaab and the battle lasted for more than an hour, according to residents of Barawe in lower Shabelle region.
Al Shabaab, an Al Qaeda-linked Somali militant group, had claimed responsibility for the Sep 21 attack on Nairobi's Westgate shopping mall, in which over 70 people were killed.