Crews quickly rescued the unnamed pilot who wasn't hurt, the officials said. The Carl Vinson was in the Celebes Sea at the time, south of the Philippines.
The jet, assigned to Carrier Air Wing 2, was conducting "routine flight operations" at the time, according to a statement from the U.S. Navy's 7th Fleet. It did not specify exactly when the pilot ejected, and the status of the aircraft was unclear.
The F/A-18E is the single-seat version of the Navy's "Super Hornet" jet.
Navy officials have said the Carl Vinson, intended as a show of force to North Korea, will arrive in the region next week. The carrier has been making its way from Singapore to the Sea of Japan since last week, making stops in Asia along the way.
Top U.S. officials have described the deployment as a message to North Korea as it conducts missile tests and may be planning a nuclear test.
"The incident is currently under investigation. The pilot is being assessed by the medical team on board USS Carl Vinson and there are no apparent injuries at this time," the 7th Fleet added.
The United States periodically sends aircraft carrier strike groups to waters near the Korean Peninsula to project power. The Carl Vinson took part last month in the U.S.-South Korea war games.
The Carl Vinson is accompanied by a destroyer ship with an Aegis combat system to track and intercept missiles.
--Fox News' Lucas Tomlinson and The Associated Press contributed to this report.