O'Brien found himself surplus to requirements as Newcastle rejoined the top flight and subsequently made a £350,000 move to Tranmere Rovers after a successful loan period. After Tranmere, he signed for Cork City, where he played in the UEFA Cup before returning to Bohemians in 2000 as player-coach. He enjoyed some great European nights during this season as Bohs knocked out Aberdeen and beat 1.FC Kaiserslautern. He also played a part as Bohs won the League and Cup Double before retiring as a player.