On 19 October 2002, De Jong made his debut for the Ajax first team. He scored his first goal of his senior career on 18 February 2003 in a 1–1 draw against Arsenal in the Champions League. He became a first team regular the following season, in which Ajax won the Eredivisie title. In 2004–05, his last full season in Amsterdam, De Jong was named Ajax Player of the Season. After a period when he appeared regularly in midfield, he found himself sitting on the bench more often than being in the starting line-up. On 7 December 2005, it was announced that De Jong did not wish to extend his contract with Ajax, which was due to end in July 2006.

On 31 March 2004, De Jong made his debut with the Netherlands in a friendly game against France. He was overlooked for the squad that went to play in UEFA Euro 2004, and missed the 2006 FIFA World Cup with a knee injury.

On 26 January 2006, De Jong signed a four and a half-year contract at Bundesliga club Hamburg, the transfer fee approximately €1 million. At Hamburg he joined two other Dutchmen: Rafael van der Vaart and Khalid Boulahrouz. He made his Hamburg debut two days later in a 2–1 defeat at Nürnberg. In March 2006, De Jong scored the winning goal in Bayern Munich’s first ever defeat at the Allianz Arena. The following week he received the first red card of his career for a second booking in a UEFA Cup match against Rapid Bucureşti. His season was cut short in April, when he required surgery on a knee problem. The injury also kept him out of the Dutch squad for the 2006 World Cup, though he was later put on standby after regaining fitness.

On 21 January 2009, De Jong was signed to Manchester City for an estimated fee of £18 million by manager Mark Hughes who deployed him in the role of midfield enforcer in a team whose defence badly needed reinforcement. He signed a four-and-a-half-year contract. and was assigned the number 34 shirt. He made his debut for the club against Newcastle United on 28 January 2009. He made sixteen appearances in the Premier League over the second half of the season.

De Jong was given a start against Arsenal on 12 September 2009. He was named Man of the Match by Sky Sports in a 2–1 win over Chelsea on 5 December 2009. By the end of the season he had become a firm fans’ favourite as well as being one of new manager Roberto Mancini’s first picks as defensive midfielder as the team narrowly missed out on a Champions League berth. De Jong scored his first goal for Manchester City in a 2–1 victory against West Ham United on 1 May 2011.

De Jong scored his first international goal against Iceland on 6 June 2009 in a 2010 FIFA World Cup qualifying match, which sealed the Netherlands’ passage to the 2010 World Cup.

Despite his ability, and reputation as one of the best defensive midfielders in the world at his peak, De Jong has also drawn criticism over his feisty, physical, and combative playing style, including from his former Dutch national team manager Van Marwijk. During an international friendly on 3 March 2010, De Jong fractured the leg of Bolton Wanderers’ American international Stuart Holden as the result of a late challenge. In the 2010 FIFA World Cup Final he kicked Spanish player Xabi Alonso in the chest, a challenge for which De Jong admitted he was lucky not to have received a red card. On 3 October 2010, in a Premier League match against Newcastle United, a tackle by De Jong on Hatem Ben Arfa resulted in the latter being carried off the pitch with a double fracture of his left tibia and fibula. De Jong was later dropped from the Dutch national team by his coach Van Marwijk for an unspecified period of time, but was later reprieved. During his time at Manchester City, however, De Jong was never shown a red card. Indeed, despite his reputation as an aggressive and hard-tackling player, De Jong’s first official direct card of his career came with Milan, in a 1–1 away draw against Verona in Serie A on 13 December 2015; previously, he had only been sent off once in an official game, namely for two bookable offences in a match for Hamburg against Rapid Bucharest in the 2005–06 edition of the UEFA Cup, while his only direct red card had come against Werder Bremen, in the semi-finals of the 2006 DFL-Ligapokal. In April 2016 while playing for the LA Galaxy De Jong was involved in another controversial incident when a strong takedown led to Portland Timbers midfielder Darlington Nagbe being removed from the field with an injury. The tackle led to a 3-game suspension for De Jong after the disciplinary committee determined the action to have been, “a clear and unequivocal red card.”

De Jong was a member of the City side which won the 2010–11 FA Cup and the 2011–12 Premier League, making 137 appearances and scoring twice before being sold to A.C. Milan in August 2012.

On 31 August 2012, De Jong joined Italian club Milan for £3.5 million rising to £5 million depending on appearances, signing a three-year deal. On 1 September, De Jong made his debut against Bologna. De Jong scored his first goal for Milan in a 3–2 loss against Lazio on 20 October.

In January 2012, De Jong signed a four-year deal with football boot brand Puma.

In December 2013, Spanish football website El Gol Digital ranked De Jong tenth in its list of the world’s dirtiest footballers. This style of play earned him a title as the most violent footballer in the world, according to French newspaper L’Équipe.

On 4 May 2014, De Jong scored his second goal for Milan, the winning goal against Inter Milan in the Derby della Madonnina at the San Siro.

On 26 June 2015, Milan announced De Jong had signed a contract extension to keep him at the club until 2018.

On 31 January 2016, it was reported that De Jong had negotiated to terminate his contract with Milan and joined LA Galaxy on a free transfer, signing a one-year deal. De Jong was involved in a controversial incident in a game against the Portland Timbers on 10 April 2016 when a strong tackle by De Jong left Darlington Nagbe injured and in need of treatment. De Jong was only shown a yellow card by referee Allen Chapman, but was later suspended for three games. De Jong received a red-card after a bad tackle on Blas Perez on 5 July 2016, although with a man down, the Galaxy was still able to hold on for the win over Vancouver Whitecaps FC.

On 31 August 2016, De Jong signed for Turkish outfit Galatasaray on a two-year deal. On 5 January 2018, his contract was terminated by the Turkish club.

On 5 January 2018, De Jong agreed a free transfer to Bundesliga side Mainz 05.

In July 2018, De Jong moved to Qatari club Al Ahli.

In July 2019, De Jong moved to Qatari club Al-Shahania.