After a slow start due to injuries, Pilkington became an ever-present in the Luton defence and helped the club win the 2009 Football League Trophy.

[5] He became one of the first names in the first XI during his first season, alongside captain and centre-back partner Sam Collins, making 49 appearances in the 2003–04 campaign.

[11] The 2006–07 season was a 'topsy-turvy' campaign, as Pilkington captained his side to a mid-table finish, with a decent League Cup run to boast about – besting Championship sides Preston North End, Queens Park Rangers and Norwich City – before taking Premier League Tottenham Hotspur to extra time.

[16] A series of recurring injuries picked up throughout the season limited his playing chances, though he returned for the final run-in of games on 17 March 2009.

Pilkington played in the Luton side that beat Scunthorpe United 3–2 in the Football League Trophy final at Wembley Stadium.

[21] He missed the start of the 2011–12 season due to injury but returned to the first-team in October and played 33 league games to help the club secure the place play-off position.

[23] In June 2012, Pilkington signed for Mansfield Town, who finished above Luton in the Conference Premier the previous season but also lost in the play-offs.

[24] Mansfield won promotion into the Football League as Conference champions in 2012–13, though Pilkington was the club's "forgotten man" with only four appearances to his name.

[25] In August 2013, Pilkington joined Conference Premier side Forest Green Rovers in a two-month loan deal.

[31] He was released by Mansfield at the end of the season, and signed with Macclesfield permanently in July 2014 after manager John Askey described him as a "proper pro".

[32][33] He missed just two league games of the 2014–15 season as Macclesfield finished one point outside the play-off places, and he was voted the club's Player of the Year.

[36] He made 54 appearances across the 2016–17 campaign, including in the 2017 FA Trophy final at Wembley Stadium, where Macclesfield were beaten 3–2 by York City.

[39] Pilkington retired from playing in June 2018 to take up the position as first-team coach at League One side Shrewsbury Town, having been recruited by former Macclesfield manager John Askey.