The F/A-18E Super Hornet was making its approach to the USS Carl Vinson off the Southern California coast about 10 p.m. Wednesday when it went down, Navy spokeswoman Lt. Reagan B. Lauritzen said.
"The pilot ejected from the aircraft, was recovered safely and is currently aboard Carl Vinson in stable condition," she said.
Lauritzen said she didn't have any more information on the pilot's condition.
Other aircraft from the vessel still in the air were safely diverted to the naval airstrip at the Coronado section of San Diego.
Lauritzen said the cause of the crash will be investigated. The Hornet has not been recovered from the sea.
The craft was assigned to a squadron based at Naval Air Station Oceana in Virginia.
It was the second military aircraft crash in the California area Wednesday. In the afternoon, a Marine Harrier jet crashed in flames in a residential area of Imperial but no one was hurt. The pilot safely ejected and no one on the ground was injured.