The alligator was killed instantly in the incident, and a picture of the scene was shared on Facebook.
According to WFTV, the pilot involved was called Rick Crose, but another pilot called Brad Pierce shared the image, and called it "one of the craziest things I've seen in all my years of aviation".
The unfortunate incident happened during a night flight on 1 June, reports the Miami Herald.
Mr Pierce wrote: "I was told the pilot was flying a Navajo and the gator jumped up and struck the wing during his landing.
"The gator was killed instantly and the aircraft sustained damage to the wing."
The Orlando Executive Airport is bordered by Lake Underhill and Lake Barton, which may be where the alligator came from.
Pierce added: "I've never seen one on a taxi way or a runway. GOAA does a really nice job of ensuring there is a nice harmony and balance between nature and man and the machines that are out there. So it is insane. It is absolutely crazy to see something like this."