Commencing the season 2004–05 in the starting eleven, Kerr suffered a dip in form and only appeared another four times before making his way back into the first team at the turn of the year. He went on to miss only one more match throughout the rest of the season, and became a vital part of the midfield as Gordon Chisholm became manager. His two goals in that term came in the Cup competitions, one in the 3–0 League Cup win over Stranraer at Tannadice and the other in the thrilling 4–3 Scottish Cup tie against Gretna; he played the entirety of the final, a 1–0 loss to Celtic.