The incident occurred as the fighter jet was approaching the carrier for a landing, and the cause is currently under investigation.
The pilot, who was quickly recovered by a helicopter, is being assessed by a medical team aboard the Carl Vinson but suffered no apparent injuries, a Navy news release said.
Earlier this week, President Donald Trump said he was sending "an armada" to Korean waters potentially to deal with threats from North Korea.
In the face of recent saber-rattling from North Korea, Trump had said the USS Carl Vinson carrier group was being deployed to waters off the Korean Peninsula.
"We are sending an armada. Very powerful," Trump told Fox Business Network's Maria Bartiromo. "We have submarines. Very powerful. Far more powerful than the aircraft carrier. That I can tell you."
It turns out the carrier group was never actually steaming toward the peninsula, but rather heading to joint exercises with the Australian navy. US officials insist it's now on its way to the Sea of Japan, known in South Korea as the East Sea. It still hasn't arrived.
On Thursday, the US Navy announced it was extending the Vinson's deployment by 30 days "to provide a persistent presence in the waters off the Korean Peninsula."
Often described as the backbone of naval aviation, the various F-18 aircraft make up most of the service's strike fighter fleet.
The F/A-18 Super Hornet was designed to have a lifespan of roughly 6,000 flight hours, but today, jets are being stretched to fly between 8,000 and 9,000 hours to fulfill mission expectations as a result of fewer operational aircraft, budget restrictions and delays to the fifth-generation F-35 Joint Strike Fighter.
Trump asked Congress for an additional $13.5 billion this year in part to build and modernize additional F-35s and F/A-18s.
The Navy estimates a portion of their current F/A-18 fleet will remain in use through 2030.