He found himself to be the third choice behind Peter Schmeichel and one of Gary Walsh, Tony Coton or Raimond van der Gouw.
Pilkington made the first competitive start of his career in one of the most embarrassing games of United's modern history on 20 September 1995, when as the Premier League's second-placed team, they were beaten 3–0 at home by Second Division strugglers York City.
In February 1996, he joined Division Three side Rochdale on a six-week loan, as the arrival of Coton had reduced him to third-choice goalkeeper after six months as second-choice.
He played 17 games for the Second Division club, keeping just two clean sheets in a sub-par team that finished the season seventeen points adrift of safety from relegation.
He spent two months on loan with Scottish Premier League giants Celtic in the run-up to their 1998 title triumph, but he failed to make the field.
Unable to dislodge the veteran Paul Musselwhite in the 1998–99 season, a young Pilkington played nine Division One games in mid-season, Vale losing all but two of them.
[7] He played just three games for the "Stags" that season, before summer signing Michael Bingham from Blackburn Rovers was recruited as competition for the number 1 jersey.
Early in the season, Pilkington conceded a goal in bizarre circumstances during a League Cup First Round defeat to Notts County.
Opposition keeper Steve Mildenhall put a free kick into Pilkington's net from inside of his own half of the field.
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.
[24] Ten days later, Pilkington signed a permanent one-year contract for his previous loan club, Luton Town.
[30][31] On 29 March 2013, he took to the field as a half-time substitute after Bartosz Białkowski was taken ill, and conceded one of the goals in a 2–1 defeat to Brentford at Griffin Park.
[35] He registered as a player at the Abbey Stadium for the 2018–19 season and was named on the substitutes bench in a 3–2 win over his former club Notts County on 11 August.
[36] He joined Barnsley's coaching staff in July 2019, leaving him at a club two division higher and closer to his Lincolnshire home.