 Pilkington started the 2009–10 season well, scoring on the opening day of the season against Southend United when Huddersfield were two goals down to make it 2–1, they eventually drew the game 2–2.He then scored two more in the second round of the Football League Trophy in a 3–3 draw with Chesterfield, eventually losing on penalties.His second league goal came in a 2–1 away loss at Charlton Athletic with a 30-yard free kick just before half time.