The buck was photographed by a lighthouse keeper who was on the island.
Tony Diamond, a researcher at the University of New Brunswick, has logged a significant amount of time on the island over the years studying the local puffin population.
He said he was "gobsmacked" when he saw the photo of the deer on the island.
"You get a few seal pups that appear every spring. There is often a bat or two when we arrive in early May. They don’t tend to last the summer," he said.
"There are no mammals other than people."
Machias Seal Island is roughly 20 kilometres southwest of Grand Manan and 16 kilometres southeast of Cutler, Maine.
Diamond said he has no idea how a deer would swim that far and make it on the island.
"It is either an extremely Olympic-class swimming deer or somebody’s idea of a practical joke," he said.
"I don’t know whether a lobster fisherman might have decided this would be funny and it would hit the news. But that’s never been recorded before, for sure."
Joe Kennedy, a biologist with the Department of Natural Resources, said he expects the "healthy, six-point buck" came from the United States.
"It is likely an American deer. And of course, the coastal tides are quite strong flowing in between Maine and Grand Manan, so it is likely that the deer came off the Maine coast and was flushed down toward Machias Seal Island," Kennedy said.
He said deer hair are hollow, so they float very well.
What Kennedy found particularly interesting is that the deer didn't spend more time on the island.
"It is just surprising to me that it didn’t stay on the island longer, just to take a rest and get some food," he said.
The ownership of Machias Seal Island is disputed between Canada and the United States.
The tiny island is known for its puffin population.
Correction : An earlier version of the story said the Machias Seal Island is located in the Bay of Fundy.(Nov 18, 2014 2:53 PM)