He started the 2008–09 season as second choice keeper behind Russell Hoult. Following an injury to Hoult, Pilkington made 26 appearances as his club struggled yet again. The ten points that Notts County finished above 23rd-place Chester City concealed the fact that, without point deductions for other teams, the "Magpies" would once again have finished six points above the relegation zone. After a takeover at County in the summer of 2009, Pilkington found himself out in the cold as third choice goalkeeper behind new signing Kasper Schmeichel and, once again, Russell Hoult. On 12 November 2009, he signed on a one-month loan for Conference Premier side Luton Town, later extended for a further month on 17 December, acting as cover for the injured Mark Tyler. He returned to Notts County after suffering an injury of his own in a 3–2 loss to Ebbsfleet United on 30 January 2010. On 10 May 2010, it was announced that he had been released by Notts County along with seven other players.
