After four days of racing on the Curlane Bank and outside Cork Harbour, the Dubliner finished the ten-race light-air event on a tally of 16 points to the Crosshaven boy's 17.
Anthony O’Leary was the Race Officer for the Main Fleet and Barry Rose officiated for the Regatta Fleet.
Flynn's club mate, 14-year-old Rocco Wright, finished in third on 30-points in the 79-boat main fleet.
The National Yacht Club's Clementine van Steenberge was the first girl in fifth overall.
The fight for gold in the 36-boat Junior Championships came down to who beat who in the final race and the NYC's Caoilinn Geraghty-McDonnell beat Des Turvey of Howth with Riona McMorrow Moriarty in third.
A 34-boat Regatta fleet was won by RCYC's Ethel Bateman who beat her brother Olin. Third place went to Henrietta Leech from Lough Ree Yacht Club.
Prizes were presented by Royal Cork Admiral Colin Morehead, event organiser Brian Jones and IODAI President Tim Lucas.
Overall results are here