After picking up a hip injury during the 2011–12 pre-season he missed all the pre-season games, to return against his former club Newcastle United. Then stepped up his recovery against Leicester City in a behind closed doors friendly. The summer also saw O'Brien take the number 5 shirt after previously occupying the number 40 shirt. O'Brien started for Leeds the opening day of the season as they crashed to a 3–1 defeat against Southampton, with O'Brien at fault for the second goal when his backwards header was converted by Adam Lallana. He was given a torrid time against his former club Bradford City and was substituted to loud jeers in the second half with Leeds 2–1 down. Leeds went on to win the game 3–2. O'Brien dropped out of the Leeds squad for the following game on 13 August against Middlesbrough in a match Leeds lost 1–0.