After loan spells with Sheffield Wednesday and West Ham United, Johnson left Wolves by mutual consent, and spent the latter part of the 2014–15 season with Charlton Athletic.

Johnson spent time at Portsmouth and AFC Bournemouth before joining Wycombe Wanderers as a 15-year-old, where he developed through the club's youth system.

[4] He made his first-team debut for Wycombe in the final game of the 1999–2000 season against Cambridge United,[2] becoming the youngest ever player to make a Football League appearance for the club at the time, at the age of 17 years and 8 days.

[4] The following season, Johnson also made one substitute appearance, and was on the bench as Wycombe beat Premier League club Leicester City in the FA Cup quarter-finals.

[4] After the departure of Adams after one season (6 months), Johnson became a regular in the side and was handed the captaincy by new manager John Gorman when he took over in November 2004, as well as finishing second in the player of the year award to forward Nathan Tyson.

[6] Johnson had a strong first year at Cardiff, and after spending the first six months as a regular substitute, began to form a dominant pairing with Dutchman Glenn Loovens which saw them keep club captain Darren Purse out of the side.

[14] The summer transfer window saw prolonged interest in Johnson; both Ipswich Town and West Bromwich Albion had bids rejected.

Despite continued changes in his defensive partner, having played alongside Loovens, Purse and new signing Gábor Gyepes, who forced his way into the side past Purse in November,[16] Johnson passed 100 appearances for the club, and had played every minute of the season[17] until he had to leave the field during a 2–0 victory over Crystal Palace on 11 April 2009, after being hit in the throat by an elbow from Palace defender Claude Davis.

[28] Johnson's header set up the opening goal for Nikola Žigić as Birmingham City defeated favourites Arsenal 2–1 to win the 2011 Football League Cup final.

[32] Johnson was almost immediately handed the captaincy of Wolves by Mick McCarthy shortly before the start of the new season, relieving former captain Karl Henry of his duties.

[41][42] No sale took place during the summer transfer window, and on 16 September, Johnson joined Championship club Sheffield Wednesday on loan for three months.

[45] Johnson played six games in all competitions for West Ham, his first coming on 8 January 2014 in a 6–0 away defeat to Manchester City in a semi-final of the League Cup.

He made his debut on 14 October in an FA Cup fourth qualifying round match away to Dover Athletic,[56] playing until the 90th minute and helping his team achieve a goalless draw.

[57] Johnson helped Bromley reach the FA Trophy final at Wembley Stadium against Brackley Town, however he conceded an own goal in the 95th minute.