Gardaí said the man has been charged with a count of criminal damage and is due to appear at Waterford District Court on 6 July.
Gardaí had been investigating the incident where a number of Pride flags were taken down and set alight at the Mall, Waterford city in the early hours of Monday morning last.
The incident came at the end of Waterford's Pride of the Déise weekend for the LGBTQ+ community.
Re-flying the flag
Meanwhile this afternoon, people gathered today for the re-raising of Pride flags outside Waterford City and County Council's buildings at the Mall, where activists, politicians and gardaí saw the flag held aloft again.
"Being able to be visible is a really important thing to do because we get knocked down but we stand back up," said Debbie O'Rourke, from the Pride of the Déise group.
"We really think of the LGBT people across Waterford who wouldn't be able to stand here and be proud and we want this to be a really clear message that LGBT people are part of communities in Waterford."
Inspector Gavin Hegarty, from Waterford Garda Station, said it was important for gardaí to show their support for the event.
"For us [Pride is] one of our biggest months of the year, coming together as a community to support everybody. It's important for us to support all members of our community no matter what their background or whatever their views on the world might be."
Mayor of Waterford Cllr Damien Geoghegan said it was crucial that the flags be flown again. "I'd much prefer not to be here today," he added, "but Waterford is a very warm inclusive place, it's a great place to be, it's a great place to live."