The Iranian Shahed-139 drone was flying toward the carrier "with unclear intent" and was shot down by an F-35 US fighter jet, it said on Tuesday.
"An F-35C fighter jet from Abraham Lincoln shot down the Iranian drone in self-defence and to protect the aircraft carrier and personnel on board," said Navy Captain Tim Hawkins, a spokesperson at the US military's Central Command.
No American service members were harmed during the incident and no US equipment was damaged, he added.
The incident came as diplomats sought to arrange nuclear talks between Iran and the United States, and US President Donald Trump warned that with US warships heading toward Iran, "bad things" would probably happen if a deal could not be reached.
The Lincoln carrier strike group is the most visible part of a US military build-up in the Middle East following a violent crackdown against anti-government demonstrations last month, the deadliest domestic unrest in Iran since its 1979 revolution.
Trump, who stopped short of carrying out threats to intervene during the crackdown, has since demanded Tehran make nuclear concessions and sent a flotilla to its coast. He said last week Iran was "seriously talking," while Tehran's top security official, Ali Larijani, said arrangements for negotiations were under way.
The US military's Central Command said in another incident on Tuesday, hours later in the Strait of Hormuz, Iran's Islamic Revolutionary Guard Corps forces harassed a US-flagged, US-crewed merchant vessel.
"Two IRGC boats and an Iranian Mohajer drone approached M/V Stena Imperative at high speeds and threatened to board and seize the tanker," Hawkins said.
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