On November 6, 1986, Sir Alex Ferguson was named manager of Old Trafford. He won 38 trophies over his 26 years with Manchester United, including 13 Premier League crowns, five FA Cups, and two UEFA Champions League titles. For his contributions to the game, he was knighted in the Queen's Birthday Honours list in 1999. Ferguson is Manchester United's longest-serving manager, having surpassed Sir Matt Busby's record on December 19, 2010. He stepped down as a manager at the end of the 2012–13 season, after winning the Premier League in his final season. His most successful time as United manager, though, was from 1999 to 2009.

Coach: Sir Alex Ferguson

Trophies: 2 Champions League (1998–99, 2007–08), 7 Premier League titles (1998–99, 1999–2000, 2000–01, 2002–03, 2006–07, 2007–08, 2008–09), 2 FA Cups (1998–99, 2003–04), 2 League Cups (2005–06, 2008–09), 3 Community Shields (2003, 2007, 2008), 1 Intercontinental Cup (1999), 1 FIFA Club World Cup (2008)

Star Players: Eric Cantona, Peter Schmeichel, Roy Keane, Paul Scholes, Ryan Giggs, David Beckham, Stam, Dwight Yorke, Ruud van Nistelrooy, Rio Ferdinand, Nemanja Vidic, Wayne Rooney, Cristiano Ronaldo, Carlos Tevez, Edwin van der Sar

Finalists, Manchester United and Bayern Munich were placed together in Group D of the 1998-99 UEFA Champions League, together with Spanish champions Barcelona and Danish champions Brondby IF, in what became known as the "group of death." Manchester United faced Inter Milan, the Group C champions, in the quarter-finals. United won the first leg 2–0 at Old Trafford thanks to two goals from Yorke. Inter's Nicola Ventola equalised in the second leg, but Paul Scholes' late away goal ensured United's advancement to the semi-finals. In the semi-finals, United were up against Juventus, another Italian team.

After Antonio Conte put Juventus ahead midway through the first half, Giggs struck in injury time to salvage a 1–1 home draw for Manchester United. Filippo Inzaghi scored twice in the first 11 minutes to put Manchester United down in Turin. Before halftime, goals from Keane and Yorke levelled the game but gave United the lead on away goals, with Cole scoring the game-winning goal seven minutes from time. On May 26, 1999, Manchester United and Bayern Munich faced off at Camp Nou to determine the victor of the 1998–99 UEFA Champions League. Manchester United won 2–1 thanks to goals from Sheringham and Solskjr in injury time, cancelling out Mario Basler's early strike.

United's success under Sir Alex Ferguson continued after the Treble, with back-to-back Premier League wins in 1999-00 and 2000-01. However, in the next years, the Treble-winning team would be disassembled piece by piece. United failed to retain the Champions League the following season, losing in the quarterfinals to eventual winners Real Madrid. United's rebuilding process has begun. United immediately bolstered their roster with the additions of Kleberson, Djemba-Djemba, David Bellion, and Cristiano Ronaldo. United continued to fall behind Arsenal and Chelsea in the standings, finishing third. Despite their Premier League tragedy in 2003/04, United did reach the FA Cup final, when they defeated Millwall 3-0.

Wayne Rooney was the most expensive teenager in the world when he came to Old Trafford from Everton early in the 2004-05 season. In June 2005, Edwin van der Sar arrived from Fulham, eventually giving the club a worthy successor to Schmeichel. United were defeated once again in the Premier League, with Chelsea, backed by Roman Abramovich, looking ready for a spell of domestic domination. United's fortunes were finally turning around before the start of the 2006-07 season, after three seasons without a Premier League title. Although Van Nistelrooy moved to Real Madrid, the emergence of Ronaldo as a world-class player was crucial for United. Rooney and Ronaldo's striking relationship was quickly developing into a dangerous one.

United had a strong start to the season, winning their opening four Premier League games for the first time since 1985. From the tenth match of the 38-game season, they established the early pace in the Premier League and never relinquished first place. Manchester United went on to win their ninth Premier League title, but Chelsea's Didier Drogba scored a late goal in the FA Cup final at Wembley Stadium to deny them a record-breaking fourth double. In the Champions League, the club advanced to the semi-finals after defeating Roma 7–1 at home in the second leg of the quarter-final but fell 3–0 to Milan in the second leg of the semi-final after leading 3–2 after the first leg.

In the summer of 2007, Nani, Anderson, Owen Hargreaves, and Carlos Tevez all arrived at Old Trafford. Ferguson guided Manchester United to their eleventh Premier League victory on May 11, 2008. Scholes struck a magnificent goal in the Champions League semi-final against Barcelona, and United would face Chelsea in the final for the second time, this time for European glory. United would have another chance forty years after Sir Matt Busby led his squad to the European Cup. With a fantastic header from a Wes Brown cross, Ronaldo gave United the lead in the first half. Chelsea, on the other hand, fought back, and Lampard equalised in the final minutes of the first half.

The game concluded in a 1-1 tie, resulting in a memorable period of extra time. As the extra time came to a close, the teams were still tied at 1-1. Due to Cristiano Ronaldo's penalty miss, Chelsea would have won the trophy if John Terry's spot-kick had been converted, but Terry missed his penalty, and in the end, it was Edwin van der Sar's blocking of a Nicolas Anelka penalty that gave Manchester United the trophy for the second time under Ferguson and the third time overall. They also became the first team to win the FIFA Club World Cup, defeating LDU Quito 1-0 in the final.

United did make it to back-to-back Champions League finals, this time in Rome against Barcelona. However, there was little United could do to halt the Spanish giants, as they were crushed 2-0 after being outrun by their opponents. Ronaldo departed the club soon after to join Real Madrid for a reported £80 million. The following season, Wayne Rooney rose to the occasion well, and a second league title in 2010/2011 re-established United as England's best club, though they remained a long way behind Barcelona, as the 2011 European Cup Final demonstrated. So, after losing in the European final, the final season of a highly successful decade concluded with the sadness of losing their star player.