[citation needed] He started playing at Deans Sports in Swinton before going on a successful trial at Manchester United at the age of nine.
[6] On 19 August 2006, McAllister scored his first senior goal to inspire a Wednesday comeback, as they went on to beat Plymouth Argyle 2–1 at Home Park following his 52nd-minute equaliser.
[8] He would rarely feature in the rest of the 2006–07 season, only making one substitute appearance under Paul Sturrock's successor Brian Laws.
[9] After failing to feature for the first team during the start of the 2007–08 season, he was sent out on a one-month loan to League Two club Mansfield Town in September 2007.
[citation needed] He then joined Chris Casper's Bury on loan in November 2007,[13] and remained at Gigg Lane for two months without making a first-team appearance.
[17] He became a first-team regular in the 2008–09 season, making 42 appearances and claiming three league goals against Preston North End, Crystal Palace, and Reading.
[24] He was named as Shrewsbury's Player of the Month for August 2010,[25] but found first-team opportunities harder to come by in the second half of the season due to a hernia injury and the arrival of new signings Nicky Wroe and David Davies.
[35] In October 2012, he went on trial at Port Vale,[36] after personally ringing manager Micky Adams to enquire about a vacancy in midfield created when Doug Loft picked up an injury.
[39] He made his debut from the bench at Vale Park on 17 November, replacing Rob Taylor 74 minutes into a 2–2 draw with York City.
[40] However, he would only feature twice more for Vale,[40] and left the club on 8 January 2013, with Adams saying "it's unfortunate we weren't able to offer Sean more first-team opportunities, but that underlines the competition for places we have among the squad, but he's a great kid, a model professional and I'd recommend him anywhere.
[44] He made 43 appearances in the 2013–14 season[45] as Scunthorpe won promotion as divisional runners-up,[46] and was also crowned the club's Player of the Year for his "high energy and consistent performances".
[49] However, after Mark Robins replaced Russ Wilcox as manager, McAllister found first-team football hard to come by in the second half of the 2014–15 season.
[52] On 23 June 2016, McAllister signed a two-year contract with newly promoted League Two club Grimsby Town on a free transfer.
[66][67] He featured 26 times in the 2020–21 campaign and was an unused substitute as Newtown beat Caernarfon Town in the play-off final to secure qualification into the newly created UEFA Europa Conference League.
[70] Port Vale assistant manager Mark Grew said that "he's a good passer, he has excellent vision and great energy".