FC Flora was one of four clubs from Estonia that had teams playing during Gothia Cup 2013. They participated with one team in Boys 12. In addition to FC Flora, 164 other teams from 37 different countries played in Boys 12. They were divided into 41 different groups, whereof FC Flora could be found in Group 3 together with Delhi Public School 1, Kista SC 2 and IFK Fjärås 1. FC Flora continued to Play off A after reaching 1:st place in Group 3. In the playoff they made it to 1/16 Final, but lost it against Halmstads BK with 2-5. In the Final, KF Gjakova won over Halmstads BK and became the winner of Play off A in Boys 12.