The strike took place in southern Somalia, US defence officials said, without revealing further information, such as the identity of the suspect or whether the strike was believed to have been successful.
Another US official said the operation took place in a remote area near Barawe, a militant stronghold on Somalia's southern coast.
The port town was the site of a failed raid by American commandos last October targeting a militant known as Ikrima.
The US forces pulled out after a gun battle without capturing Ikrima, described as a planner and operator who has relentlessly plotted attacks on neighbouring Kenya.
Al-Shabaab has been weakened by African Union troops over the past two years, which has brought some stability to many parts of Somalia after a campaign of cross-border raids and kidnappings of Westerners and security forces.
The rebels, who have waged a seven-year insurgency seeking to impose sharia law in Somalia, were behind last September's attack on a Nairobi shopping mall, killing at least 67 people.