On 29 June 2001 he signed for Blackburn Rovers permanently for a transfer fee of £1.5M. He made his Premier League debut on 22 August in a 2–2 draw with Manchester United at Ewood Park. Three days later he scored Blackburn's first goal in a 2–1 home win over Tottenham Hotspur. He made a total of thirteen league appearances in the 2001–02 season as Blackburn finished in tenth place. He was an unused substitute when Blackburn won the 2002 Worthington Cup, beating Tottenham 2–1 at the Millennium Stadium, Cardiff, on 24 February 2002. After just two league appearances, in the 2002–03 season, on 20 January 2003 Mahon was sent on loan to Second DivisionCardiff City for the rest of the season as the Bluebirds won promotion to the First Division. On 8 September 2003 he was loaned out to Ipswich, where he made eleven league appearances and scored one goal against Bradford in a three-month loan spell. He returned to Blackburn on 22 December, and made three further league appearances.
Mahon signed for Wigan Athletic on 6 February 2004, stating that he wanted regular first-team football. He made his debut the following day in a 3–1 victory over Ipswich Town at Portman Road. The following season he made 27 league appearances scoring seven goals as Wigan won promotion to the Premier League. After starting the 2005–06 season in the first team, he dropped out of favour halfway through the campaign and was allowed to leave, despite being seen as an ongoing squad player by Paul Jewell. On 23 March 2006 he joined Burnley on loan for the rest of the 2005–06 season, making his debut the following day against Norwich City. Jimmy Bullard, a Wigan Athletic player, said that all the players wore black armbands when Mahon left the club.
Burnley
After eight appearances on loan, he joined Burnley permanently on 8 June for £200,000 on a three-year contract. Burnley's then-manager Steve Cotterill described Mahon as "an absolute gem, the jewel in our crown" and it appeared that Cotterill planned to build Burnley's team around Mahon in the 2006–07 season; however, injuries and a loss of form during the 2006–07 season saw Mahon become a fringe first-team player. In the 2007–08 season, he returned to the first eleven and appeared to have regained the form that he showed when first arriving at Turf Moor. However, injuries plagued his season once again, and he started just 15 games, scoring one goal. The 2008–09 season started the same way, with his being a fringe squad player for the Clarets. On 14 March 2009, Cotterill's successor as Burnley manager, Owen Coyle, stated that fellow Championship club Blackpool had made an enquiry to take Mahon on loan for the rest of the season, saying, "I won't stand in his way because Alan needs to play. He is a terrific professional who I have so much time for and I am trying to do right by him." Blackpool caretaker managerTony Parkes confirmed Blackpool's interest in Mahon. Three days later he joined the Tangerines on loan until the end of the season. He made his debut on 21 March in a 1–1 draw with Southampton at Bloomfield Road. In June 2009 Mahon was released by Burnley at the end of his contract, alongside Gabor Kiraly and Steve Jones.
Tranmere Rovers
On 6 July 2009 he signed a three-year contract with former club Tranmere Rovers. He scored his first goal for Tranmere in a 3–2 defeat against Walsall on 12 September 2009. In July 2011 and following a series of injuries that kept him out of the first team for the whole of the 2010–11 season, Mahon's contract with Tranmere was terminated by mutual consent.
