After beginning his career with Tottenham Hotspur, Maher moved to Southend United on a free transfer on 23 January 1998. He quickly broke into the first team, making 18 appearances for the first-team that season. During the 1998–99 season, Maher scored his first career goal in a 1–1 draw with Rochdale. Over the next ten years Maher was a virtual ever-present for Southend, rising to be team captain and subsequently club captain. During this time he made more than 400 appearances for the club, and captained Southend to promotion twice, from League Two to the Championship, in successive seasons. When, during the 2007–08 season it became clear that Maher was no longer an automatic first choice he chose to look for opportunities elsewhere. He left Southend just before he would have become entitled to a testimonial, to join fellow League One side, Gillingham, on loan for the remainder of the season. In his two months with the Kent club, he made seven total appearances but did not score a goal.
In the summer of 2008, Maher joined Oldham Athletic after he was released by Southend, despite the confidence from Gillingham that he would sign with their club. He immediately signed a one-year contract with the club. On 9 August, he made his debut for Oldham in a 4–3 comeback victory versus Millwall. He later scored his first goal for Oldham on 14 March 2009 versus Milton Keynes Dons. In the 4th minute, he scored from a free kick to give Oldham a 1–0 lead, though the team lost the game 6–2. On 13 May, under new manager Dave Penney, Maher's contract was not renewed, resulting in his release from the club.
Gillingham
In June 2009, he joined Gillingham on a two-year deal.
In June 2014 Maher was appointed head coach of Chelmsford City. On 14 February 2015, Maher was an unused substitute in the Clarets' 2–0 defeat to Maidenhead United. In October 2015 Maher returned to Southend in a coaching capacity, assisting the under 21 and youth teams at the club and at the end of November 2015, he was appointed U21 manager of the club. On 20 January 2016, Maher was named as Chelmsford City's caretaker manager after previous manager Mark Hawkes left the club, On 26 February 2016, Maher was appointed Chelmsford City manager until the end of the season, before being replaced by Rod Stringer during the summer break. In July 2019, Maher left his position at Southend and joined Bristol Rovers as a first team coach.
