Gary Johnson signed for Watford as an apprentice at sixteen and turned professional at the age of eighteen. He then left Vicarage Road and moved to play football in Sweden for a second division side.
After building up a successful football holidays business, Johnson then returned to England and played part time football too for both Newmarket Town and Cambridge United.
After his playing career ended, Johnson would spend the next six years training to earn his coaching badges and he took his first managerial job at Newmarket Town in 1986.
Johnson was manager at Newmarket Town, when he was persuaded to join Cambridge United as reserve team manager in 1988. Appointed as assistant manager in 1990, Johnson helped John Beck organise the U's remarkable rise in the early 1990s, in which they came within two matches of becoming the second club to rise from the old Fourth Division to the top flight in successive seasons (after Northampton Town in 1966). Johnson was briefly caretaker manager in late 1992 and then took charge from 1993 until 1995. Under Johnson's stewardship, the U's were contenders for a play-off place in Division Two in 1993–94, before eventually finishing tenth.
The following season, many players were sold in order to balance the books and Johnson moved to take over at Kettering Town.
After leaving Cambridge, Johnson took over as manager of Kettering Town as the club introduced full-time football for the first time in the club's history. However, once the decision was made to revert to being a part-time club, Johnson moved to Watford as director of their youth academy by request of future England manager Graham Taylor.
He was approached by the Latvian football authorities for help, and became coach of their national team for two years from 1999 to 2001.
Whilst coaching Latvia, he spotted the potential of Marian Pahars and recommended him to Southampton's manager Dave Jones, who invited Pahars for a trial before signing him in March 1999. He also recommended Igors Stepanovs to Arsenal manager Arsène Wenger
His contract expired and Johnson returned to England during the summer of 2001 to take over as manager of non-league side Yeovil Town.
In his first year in charge at Huish Park, the Glovers won the FA Trophy by beating Stevenage 2–0 in the final at Villa Park as well as finishing third in the Football Conference; the following year they won the greater prize of the Conference championship by a record margin of seventeen points and topping the hundred goals mark too, winning promotion to the Football League. Yeovil were immediately contenders in the League and after their debut season ended by missing out on the playoffs by goal difference, they were Division Three champions at the second attempt, scoring ninety goals in the process.
During a League Cup game against Plymouth Argyle, Johnson's son (Lee Johnson) accidentally scored a goal after attempting to play the ball back to Argyle's keeper (who had kicked the ball out because of an injury to a Plymouth player). In a show of good sportsmanship Gary Johnson told his players to allow Argyle to walk the ball into the net to level the score at 1–1, avoiding controversy. Yeovil went on to win the game 3–2, with Lee Johnson scoring a hat-trick.
Despite turning down an approach from Derby County in the summer of 2005, Johnson became Bristol City's target when their manager Brian Tinnion resigned that September. Yeovil agreed compensation terms and he became City's manager on 26 September 2005. Despite their lowly position of 22nd in the table, City's fortunes turned around under Johnson and a great run of form in the second half of the season saw them in play-off contention, eventually finishing ninth after a run of 55 points from 36 games.
Johnson won the League One Manager of the Month award for April 2006. After an impressive 2006–07 season (including an 18 match unbeaten run), Johnson won the award again in March 2007 after successfully guiding his side to 16 points from seven games the previous month. This had set Bristol City in a good spot to contend for automatic promotion, which they sealed on 5 May 2007 with a 3–1 home win over Rotherham on the last day of the season.
On 6 September 2007, Gary Johnson and assistant Keith Millen both signed 2 and a half year contract extensions keeping them at the club until 2010.
In the 2007–08 season, he kept Bristol City in the top six of the Championship for almost the entire season and in the top two for a long time; the team were the surprise package of the season. Bristol City eventually lost the play-off final to Hull City at Wembley and were not promoted to the Premiership. Johnson made his players stay on the pitch after the match and watch the Hull City players celebrate as a motivational experience for the next campaign.
In the summer before the 2008–09 season, he broke the club record for a transfer fee in signing 21-year old Nicky Maynard from Crewe Alexandra for £2.25 million.
Bristol City's famous chant of 'Johnson says bounce around the ground' was inspired by Gary Johnson who was quoted to saying in an interview before a league game that he wanted the fans bouncing around.
In September 2008, Johnson signed a new five-year contract with Bristol City, to keep him at the club until 2013. The club ended the season with another top ten finish and on 18 March 2010, with the club comfortably in mid table, the club issued a statement that Johnson had "left his post as manager of Bristol City by mutual consent".
He was appointed manager of Peterborough United on a two-year contract on 6 April 2010.
With the club lying in the playoff positions, Johnson left Peterborough on 10 January 2011. The reasons are that the manager and the chairman could not agree future policy.
On 4 March 2011, Johnson was announced as the new manager of Northampton Town signing on a two and a half year deal His first season in charge saw Johnson save the club from relegation from the Football League beating Stevenage in the penultimate game of the season. Northampton Town and Johnson parted company by mutual consent on 14 November.
On 9 January 2012, Johnson returned to former club Yeovil Town, replacing Terry Skiverton who became Johnson's assistant. The Glovers, with Johnson at the helm, produced an impressive run of form with thirty points in nineteen games to reach safety with two games still left to play.