Having spent his youth career at Everton, Pilkington made his senior debut at Exeter in 2002, during a loan spell. Going on to leave Everton, he joined Port Vale in 2003 and played more than 250 games for Vale. In 2008 he joined Luton, where he stayed for four years, then in 2012, he signed for Mansfield.
Following spells with Luton and Forest Green, eventually earned Pilkington a loan move to Macclesfield in 2014. After signing a permanent contract with the club, Pilkington has become a first team regular as well as a fan favourite, being named ‘Player of the Season’ in each of his three full seasons at the Moss Rose and signed a new one-year contract in the summer of 2017.