CIA director William Burns was in Mogadishu on Thursday, the office of Somali President Hassan Sheikh Mohamud's office said on X.
Somalia said the two "discussed regional issues of mutual interest and enhancing Somalia-US strategic partnership in critical areas, including the fight against international terrorism".
Mr Burns, a former diplomat who was a deputy secretary of state in the Obama administration, visits Somalia at a time of heightened tensions after Houthi attacks on commercial shipping in the Red Sea.
Last week, two US Navy Seal commandos went missing during an otherwise successful operation to intercept a shipment of Iranian arms to the Yemeni militia, off the coast of Somalia.
Since about 2006, Somalia has also been struggling with the extremist insurgent group Al Shabab, who are known for suicide attacks on civilian targets and assassination of government officials.
The group, which is also active in Kenya, rose to prominence in the chaotic aftermath of Ethiopia's invasion of Somalia, exploiting tribal divisions to gain control of parts of the country.
Subsequent military operations to destroy Al Shabab, which is thought to have had between 5,000 and 20,000 members over the years, have never succeeded in stamping out its operations.
In June, the group killed at least 50 African Union peacekeepers in a raid on their base in Uganda, and the following month, suicide attackers killed up to 40 Somali soldiers at a base in Mogadishu.
The capital was hit again last month in a suicide attack attributed to the group, killing at least five people.
Meanwhile five UN staff are thought to be held by the group after the helicopter they were travelling in crashed in a remote area, killing one.
US efforts to bolster Somali security forces since 2010, sending about $500 million in security assistance and training Somali soldiers, have also had limited effect curbing the group.
"They are training and developing Somali special forces, who are very effective," said Guled Ahmed, a non-resident scholar at the Middle East Institute.
"They are providing drones to basically deter Al Shabab and aid the Somali government, and they're providing intelligence. They see the war on Al Shabab as crucial to succeed."
Experts say high levels of corruption and political factionalism have stymied international security and development efforts to stabilise the country.
Somalia is again locked in a bitter dispute with Ethiopia over an agreement between Somaliland, a territory that broke away from Somalia during a 1991 civil war, and Addis Ababa, which would see Ethiopia gaining access to the sea from Somaliland.
“I call on Arab nations to close ranks and stand fast in the face of this Ethiopian plot and declare solidarity with Somalia," Somali Prime Minister Hamza Abdi Barre told an emergency Arab League meeting on Wednesday.
Mr Burns's trip comes as tensions rise between Somalia, Ethiopia and the self-proclaimed independent region of Somaliland.
Mr Ahmed said he believes the trip was an attempt to pressure the Somali government to "not escalate the situation".
