Mr Bryson donned the costume of 'Footie' for the World Cup qualifier against Azerbaijan in November and paraded around Windsor Park clapping and waving at supporters.
The Irish FA said the 22-year-old, who had previously been on work placement with the association, had filled in as a last minute replacement for the regular mascot, who was unavailable.
A statement stressed that it was a one-off and added that Mr Bryson had never been involved in any of the IFA's community relations projects.
"The Irish FA can confirm that Jamie Bryson was Footie mascot at the Northern Ireland v Azerbaijan game on 14 November 2012," it read.
"The regular mascot was unavailable for the game and his replacement took unwell on the afternoon of the game and Mr Bryson stood in at the last minute. This was a one-off."
Mr Bryson emerged as a leader of the loyalist Ulster People's Forum in the wake of the dispute over Belfast City Hall's flag policy.
The council voted to restrict the flying of the Union Flag to 18 designated days last December, prompting a series of protests across Northern Ireland, some of which have been followed by violence on the streets.
Footie the mascot is used by the IFA to promote local football and for a number of public relations events, including its cross-community Football For All campaign.
The costume is usually worn at matches by Ian Hughes, brother of Fulham and NI defender Aaron Hughes, but he was unavailable ahead of the Azerbaijan game.
When his replacement took ill the IFA sought a work placement volunteer and Mr Bryson, who is understood to have been going to watch the match, took up the role.
The statement from the football body continued: "Mr Bryson is not involved in, or has ever been involved in any of the Association's Community Relations projects."
When asked about it on Twitter, Mr Bryson replied: "Does it really matter?"