His first managerial post was at MLS side Colorado Rapids, when he was appointed as manager in November 2008, following a successful spell as interim head coach.

[7] Smith signed for Colchester United on a free transfer in November 1987, making his debut at the age of 18 in a 2–1 away victory at Halifax Town.

[7][10] He spent time at Aylesbury United during the 1995–96 campaign,[2] making his debut in 1–0 away defeat to Dulwich Hamlet on the opening day of the season.

[14] Smith reverted to his previous role of youth team coach when Wycombe appointed manager John Gorman on 30 November 2004.

[6] However, Smith stated his role "unexpectedly took on a different nature" as he spent more time supporting the first-team, subsequently taking the job as assistant manager.

[6] He assumed an interim head coach position during the latter half of 2008 following the resignation of his predecessor, Fernando Clavijo, with Colorado bottom of the league table.

[23] After a successful ten-game trial period, Smith was formally given the head coach position on 11 November 2008, signing a three-year contract with the club.

[23] Smith's first game in-charge as head coach was a 2–1 defeat to Chivas USA on 22 March 2009, the club's first match of the 2009 MLS campaign.

[24][25] He secured his first win as head coach a week later as Colorado beat Kansas City Wizards 2–1 at Dick's Sporting Goods Park.

The club started the season positively,[29] and ultimately secured a spot in the MLS Cup play-offs after finishing in seventh place.

[7] Smith's side beat Columbus Crew on penalties following a 2–2 aggregate draw in the play-off semi-finals,[31][32] before disposing of San Jose Earthquakes in the Conference Final courtesy of a 1–0 home victory on 13 November 2010.

[37][38][39] However, Colorado "endured a difficult season" from then onwards,[40] with the club struggling with injuries to key players such as Conor Casey, Caleb Folan, Pablo Mastroeni, Drew Moor and Jamie Smith.

[41] Smith guided the club to a sixth-place finish in the league, with Colorado defeating Columbus Crew in the first-round wild-card match.

[43][44] Five days after the defeat to Kansas City, it was announced that Colorado had opted against renewing Smith's contract at the end of the 2011 MLS season.

[46] On ending Smith's three-year tenure with the club, Colorado's managing director Jeff Plush, announced that "it would be in the best interest of both parties to move in a different direction".

[52] Smith's first game in-charge of the club was a home FA Cup tie against Notts County, played on 28 January, with Stevenage winning the match 1–0.

[56] Smith's first league game as manager was a trip to Hillsborough to face Sheffield Wednesday on 14 February, with Stevenage securing a 1–0 away victory.

[71] After a 2–1 home victory over Portsmouth in late October 2012,[72] Stevenage found themselves in second place, just a point behind league leaders Tranmere Rovers.

[83] On 12 April 2017, Smith was announced as the team's first head coach for the inaugural season of Nashville SC, a new professional club in the United Soccer League.

[86] Smith coached Nashville SC to a 12-9-13 record in USL play, good enough for a playoff appearance before being knocked out by Cincinnati FC in penalties.

Nashville also won three U.S. Open Cup games in its inaugural season, which included a victory over Smith's former club, the Colorado Rapids of MLS.

[5] On 6 March 2019, the club announced Smith would be the head coach for 2020, when Nashville SC joined Major League Soccer as an expansion team.

"As we set out to build our MLS team and (general manager Mike Jacobs) and I conducted our search throughout the game for a head coach, we always kept coming back to Gary as the first and best candidate for the job," Nashville SC CEO Ian Ayre said in a statement.