A navy spokesman said the sailor had complained of abdominal pains and was checked into the medical department on the USS Dwight D. Eisenhower where she later gave birth to a seven-pound girl.
The sailor had not previously disclosed her pregnancy, CNN reported.
Both the baby girl and her mother "are healthy and are doing well," according to an official.
"As the baby was born at sea aboard an operational unit, the main focus for the US Navy, the ship and its crew is the safety and well-being of the baby and the mother," the official said.
The official said the navy has a policy which allows expectant mothers to "remain onboard a ship up to the 20th week of pregnancy and only if the time for medical evacuation to an emergency treatment facility is less than six hours."
However, the navy was unaware of this particular pregnancy, the official added.
The woman and child were flown to Bahrain by helicopter with a medical escort, where they are receiving follow-up care.
