The 18-year-old singer - who is on a tour of North America with the boy band - admitted his fear, known as orthniphobia, stemmed from an incident when one of the feathered fiends flew through his bathroom window while he was using the toilet.
He told The Sun newspaper: "I get really nervous if pigeons are flying around before shows.
"I can't stand them after one once flew in through my bathroom window and went for me while I was having a wee. That was enough. I think pigeons target me."
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Niall's bandmate, Harry Styles, explained the group - also featuring Liam Payne, Louis Tomlinson and Zayn Malik - are rallying round in a bid to "protect" their pal.
He added: "Niall's really scared of pigeons. We have to protect him."
However, the group's flashing fans could help to take Niall's mind off the petrifying pigeons, as he recently admitted One Direction's America supporters are somewhat over-zealous.
He said: "We've had a few flashers - but we're not encouraging it, or deterring it!
"The craziest thing was supporting US boyband Big Time Rush - all the fans were wearing our T-shirts and holding One Direction banners, too."