Gardaí took the flag from the fan as he waved it on the field while crowds occupied the field.
The person in question also posed with it for a picture by a professional photographer.
At least four Confederate flags were visible among Cork supporters on the Town End terrace in Semple Stadium.
The Cork County Board have thus far refused to comment on the practice of fans flying them at games.
Sport Against Racism Ireland (SARI) have called for the GAA to take action against the flags being permitted into their grounds, while GAA president Aogán Ó Fearghail said he personally had an issue with the flag being promoted at matches.
“The Confederate flag is not a flag I personally would be comfortable with,” he said earlier this month.
“I wouldn’t be comfortable with a Nazi symbol — it also has red. Stopping everybody coming in with a flag, I’m not sure we’re in a position to go do that. People need to take personal responsibility in these cases.”
News of Cork supporters’ association with the flag has gained attention in recent weeks following an incident in the US recently, with nine black people shot and killed by a Confederate flag-endorsing racist white man in a South Carolina church last month.