McInnes became manager of St Johnstone where he had been on the playing staff, in November 2007. He guided the club to promotion to the Scottish Premier League in 2009 and retained that status for two seasons. McInnes was appointed manager of Football League Championship club Bristol City in October 2011. Despite avoiding relegation in 2011–12, McInnes was sacked by Bristol City in January 2013 with the club bottom of the Championship. He was appointed Aberdeen manager in March 2013.
McInnes began his professional career in 1988 at Greenock Morton, where he played in 221 league games in seven seasons before moving to Ibrox, where he spent almost five years, playing in 53 league matches for the club. During his time in Glasgow, McInnes had a loan spell at English club Stockport County, where he made 13 league appearances. He was also briefly at French side Toulouse. McInnes scored four goals for Rangers, with strikes against FC Alania Vladikavkaz in the Champions League and Hearts in the league. He also scored twice against Ayr United and Dunfermline in Rangers' run to the 1996 Scottish League Cup Final, but he did not feature in the final itself.
McInnes joined West Bromwich Albion in the summer of 2000, but a cruciate ligament injury ended his season in October. He returned the following season to captain West Brom to a place in the Premier League. He also won West Brom's Goal of the Season award at the end of the promotion campaign, for his 25-yard strike against Sheffield United in the Battle of Bramall Lane.
McInnes was the first West Brom player to be sent off in the Premier League. He was dismissed in the second half of the club's first Premier League match against Manchester United at Old Trafford in August 2002. He played in the majority of West Brom's Premier League games during the 2002–03 season but was unable to prevent them from being relegated. He made 88 league appearances and scored six times for the West Midlands club.
McInnes joined Dundee United on 11 July 2003, and was immediately installed as team captain by manager Ian McCall. In his first full season at Tannadice, McInnes missed only three league and one cup game. He helped the club to a 5th-place finish in the Scottish Premier League and scored twice — his first coming in the Scottish Cup against Dunfermline and his second in a league match against Hearts. After an unsteady start to the 2004–05 season, McInnes began to take control again in the centre of midfield. He then picked up an injury with a third of the season remaining but managed to return to the first team for the Scottish Cup final at the end of the season.
In April 2006, United manager Craig Brewster announced that McInnes was free to leave the club at the end of the season, despite having a year of his contract left to run.
On 24 June 2006, it was announced that McInnes had finally come to an agreement to be released from his contract and he subsequently joined Millwall. The then-Lions boss Nigel Spackman gave McInnes the captain's armband with the comment: "Every Millwall player on that pitch should be a Derek McInnes." McInnes scored once during his spell with Millwall, his goal coming in a 3–2 defeat to Cheltenham on 26 August 2006.
McInnes left Millwall on a free transfer during the January 2007 transfer window, returning to Scotland to sign for St Johnstone late on New Year's Day. He made his debut for the Perth club on 6 January, against Ayr United in the Scottish Cup at McDiarmid Park.
International recognition came late to McInnes as he made his Scotland debut on 21 August 2002, coming on as a substitute for the last ten minutes against Denmark in a friendly. Three months later, against Portugal, he was a substitute once again, coming on midway through the first half.
McInnes was appointed manager of St Johnstone on 27 November 2007, after the previous management team of Owen Coyle and Sandy Stewart had departed for Burnley. On 2 May 2009, McInnes secured promotion to the Scottish Premier League for St Johnstone, ending their seven-year stint in the First Division.
During the 2009–10 close season, McInnes was linked with the managerial positions at West Bromwich Albion and Watford. He remained at St Johnstone, however, and in October 2009 he signed a new contract with the Perth club.
McInnes was granted permission by St Johnstone to be interviewed by Bristol City for their managerial position, alongside former Barnsley manager Mark Robins and another unnamed candidate, in October 2011. His managerial record with the Perth club was 177 games in charge, where he won 71 games, drew 53 games and lost 53 games.
McInnes was appointed manager of Bristol City on 19 October 2011. The club were adrift at the bottom of the Football League Championship, but McInnes guided City to an eight-game unbeaten run that secured their league status.
On 6 November 2012, following City's 2–0 loss to Birmingham City, McInnes gave £300 to 17 stranded fans who had their minibus tyres slashed outside St Andrew's Stadium. During the 2012–13 season, Bristol City suffered a club record seven consecutive defeats. McInnes was sacked on 12 January 2013, after a 4–0 home defeat to Leicester City left the club eight points adrift of safety. After being sacked by Bristol City, McInnes said that he was "very desperate" to succeed and that his time at Bristol City was difficult.
McInnes was announced as Craig Brown's successor on 25 March 2013, with Tony Docherty as his assistant. He officially took charge of the team after the Dundee United match on 6 April, with the current management opting to continue with their preparations for the last two games before the split. After the final game with Brown as manager, McInnes said he vowed to help the club improve by helping the city of Aberdeen to "fall in love" with its football team again.
Aberdeen remained unbeaten in September, winning twice and drawing once in the league and progressing to the Quarter-Final of the League Cup with a 5–0 demolition of Falkirk. The team's excellent form earned McInnes the Manager of the Month award for September.
The club had a positive start to 2014, taking maximum points from games against Dundee United, Kilmarnock and Hibs. At the end of the month Russell Anderson scored in the 94th minute to level the game at 2–2 and secure a point for the Dons against Motherwell at Fir Park to keep them in second place. McInnes praised his players and believed they "showed good determination to get something from the game." He was rewarded for his efforts as he picked up the Manager of the month award for February. Ahead of the League Cup final, Derek signed an extension to his contract, tying himself to the club until the summer of 2017.
McInnes made history as he led Aberdeen to the final of the Scottish League Cup against Inverness Caledonian Thistle, becoming the first manager to take the Dons to a final in 14 years. Aberdeen won the final after a 0–0 draw and a 4–2 penalty success that saw them lift their first trophy in 19 years. McInnes led Aberdeen to qualify for Europe for the first time since 2009, achieved through a third-place finish in the league campaign. However, McInnes was unsatisfied with the outcome when Motherwell beat Aberdeen 1–0 to take the second place. McInnes criticised the referee for ignoring the challenge when goalkeeper Jamie Langfield was fouled by John Sutton, which later lead to the goal scored by Craig Reid. At the end of the season, McInnes was awarded both PFA Scotland Manager of the Year and SFWA Manager of the Year.
Early in the 2014/15 season, Aberdeen progressed through two qualifying rounds of the UEFA Europa League, including an aggregate victory against Dutch club FC Groningen. Aberdeen finished second in the 2014–15 Scottish Premiership and again qualified for European competition. During the 2015 close season, despite mounting speculation that he was in talks to take over at Rangers, McInnes signed a new contract with the club keeping him at Pittodrie until 2019.
His Aberdeen team again pushed Celtic almost all the way in the Scottish Premiership title race in 2015–16, with Celtic eventually beating Aberdeen 3–2 on 8 May 2016, a match which secured the league title, with only two matches remaining. Aberdeen had begun that season winning all of its first eight league matches as well.
McInnes led Aberdeen to a third straight Scottish Premership runners-up spot in season 2016–17. His Aberdeen side also claimed its first win at Ibrox since November 1991, with a 2–1 victory on 17 May. McInnes led Aberdeen to both domestic cup finals in the 2016–17 season, losing both to Celtic. The team went on a ten-match winning steak at Pittodrie, which surpassed Alex Ferguson's Aberdeen record of nine home wins in-a-row in 1985–86 (although not a club record). He was again shortlisted for PFA Scotland Manager of the Year, but lost out to Celtic manager Brendan Rodgers.
In June 2017, Aberdeen granted pemission for Sunderland to speak with McInnes about becoming their manager, but he decided to stay with Aberdeen. McInnes and Docherty subsequently signed a 1-year contract extension, keeping them with the Dons until the summer of 2020.As of match played 16 September 2017
Scottish Second Division: 1994–95
Scottish Premier Division: 1996-97
Scottish Cup: 1998–99
Scottish Challenge Cup: 2007–08
Scottish First Division: 2008–09
Scottish League Cup: 2013–14