After beginning his career with Tottenham Hotspur,[2] Maher moved to Southend United on a free transfer on 23 January 1998.
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.
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.
[19] In January 2020, Maher was again placed in charge of the first-team after manager Garner was granted a period of extended leave for personal reasons.
[20] On 20 October 2021, Maher returned to Southend United, now in the National League, in the role of head coach, replacing Phil Brown.
[21] His opening match as manager ended in disappointment as he saw his side fall to a 3–0 defeat at fifth-placed Dagenham & Redbridge as the hosts scored three goals in six minutes.
[24] In late October 2023, Maher was linked with the vacant managerial position at Gillingham, but Southend denied the League Two club permission to approach him.