The USS Theodore Roosevelt, which was in the Gulf to launch strikes against the Islamic State group, passed through the Strait of Hormuz headed for the Gulf of Aden and the southern Red Sea.
It is being escorted by the USS Normandy, a guided missile cruiser. The US Navy said the pair will "ensure the vital shipping lanes in the region remain open and safe."
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Nine US ships are now near Yemen, where last month Saudi Arabia and a regional coalition launched air strikes targeting Huthi rebels.
The United States says it is not taking part directly in the Saudi-led strikes, but provides intelligence and logistical support.
Pentagon spokesman Colonel Steven Warren denied reports the US ships have orders to intercept Iranian vessels carrying weapons for the Huthis.
"To speculate on boardings would be premature," a US official told AFP on condition of anonymity.