Doherty was bought by Luton old boy David Pleat then Director of Football at Tottenham Hotspur for £1million in March 2000.

[9][10] However, the following season started badly when he broke his leg in a League Cup match against Torquay United in September following a challenge from Eifion Williams.

At Tottenham, Doherty eventually settled into a defensive role, and although he enjoyed probably his best spell after the turn of the year in 2003–04, he did not manage to consistently reach the form he exhibited before breaking his leg.

[12][13] He was eventually sold by Tottenham's new management team of Frank Arnesen and Jacques Santini at the start of the 2004–05 season to newly promoted Norwich City for an undisclosed fee.

Having returned to the side, he scored his first league goal for more than three years on Boxing Day 2008 in a 3–1 defeat to Crystal Palace at Selhurst Park.

Although Doherty was given the captaincy at the start of the 2009–10 season by Bryan Gunn, new manager Paul Lambert dropped him from the role immediately; and he was told he had no long-term future at the club.

He formed tight defensive partnerships with both Michael Nelson and Jens Berthel Askou and also scored seven goals in the process helping Norwich City to the League one title.

His agent Brendan Keyes was in talks with New York Red Bulls to bring Gary to MLS and a deal looked imminent but with terms not agreed Doherty stayed in England.

On 24 February 2012, Doherty moved alongside Charlton teammate Paul Hayes to Wycombe Wanderers, who at the time, sat bottom of League 1.

He recovered in April 2002, scoring his first international goal against the United States, but he missed out on the squad for the 2002 FIFA World Cup finals.