Swan's performances at the Calder Cannons were ordinary and he was perceived by some recruiters to be a larrikin with questionable kicking accuracy and work ethic, however Collingwood showed an interest in him as a potential late maturer in the mould of his father and took him at the relatively low draft pick (#58) in the 2001 AFL Draft.
Swan made his debut in June 2003 at the age of 19, though he only played three games (against Western Bulldogs, Richmond and Essendon). Swan managed just 30 games in his first four seasons in the system at Collingwood, and although he played some solid football in that time, was not regarded as outstanding. He played much of this time with Williamstown, which was then Collingwood's VFL-affiliate, and he was a member of its 2003 premiership team.
In 2006, he broke through, played 21 games and finished sixth in the EW Copeland Trophy voting. Swan mainly rotated through the midfield and moved forward when required. His first nine weeks were productive, averaging nearly 26 disposals and kicked 15 goals, before a hamstring injury suffered against Brisbane in round ten sidelined him until round 13.
2007 was considered his breakout season as he placed fourth in the Copeland Trophy and was a surprise packet at the Brownlow, leading for most of the night before finishing sixth with 20 votes.
The 2008 Copeland Trophy winner had a strong year averaging 25 disposals, seven marks, three tackles and one goal a game. Swan led the team in total disposals (590) and kicks (368), second in marks (163), and third in handballs (222) and tackles (75). He had 14 games of 25 possessions or more and kicked two or more goals on six occasions. Round 10 against West Coast was one of Swan’s best collecting 34 possessions, 10 marks and two goals. In round 14 against Sydney, he had 30 touches and 13 marks.
In the 2009 AFL Premiership Season, Swan averaged 31.8 disposals, 7.8 marks, 3.0 tackles and 5.4 inside 50s per game. He is one of the AFL's most prolific ball winners, along with being an in-and-under specialist winning the contested ball at most stoppages whilst also running hard.
In Collingwood's 2009 round 10 clash against Port Adelaide Swan obtained 48 possessions, 22 kicks and 26 handballs. This was the best disposal count in a decade and was then the third highest recorded disposals count in one match, behind Greg Williams' 53 and Tony Shaw's 50. It was a record since the length of game quarters was shortened from 25 minutes to 20 minutes in 1994, until surpassed in Round 22 2011 by Adelaide's Scott Thompson (51 disposals).
He was ranked 3rd in Total Inside 50s, 4th in Total Goal Assists, 1st in Total Kicks, 14th in Total Handballs, 1st in Total Disposals, 10th in Total Marks, 5th in Inside 50s Per Game, 13th in Goal Assists Per Game, 2nd in Kicks Per Game, 2nd in Disposals Per Game. He was voted runner up at the AFLPA MVP awards (polling 584 votes), losing to Gary Ablett (688). He was regarded as one of the front runners for the Brownlow Medal, but finished outside the top ten.
Swan was selected in the 2009 All-Australian side, but controversially as a half forward flanker, rather than as a midfielder, which is his usual position.
Swan averaged 31.8 disposals, including 19 kicks per game. On 6 September, Swan won the AFL Players Association MVP Award (Leigh Matthews Trophy) after a vote of the players. That year he was also elected as the ruck-rover for the AFL All-Australian Team. His very consistent season was a cornerstone to Collingwood's 15th Premiership, to the point of having his tattoos referenced on the Herald Sun Premiership Poster. Swan finished third in the Brownlow Medal count, having started favourite. On 31 October in the International Rules Series he won the Jim Stynes Medal. At the conclusion of the season, Swan became only the fourth ever Collingwood player to win three consecutive Copeland Trophies.
With Swan's contract at Collingwood due to expire at the end of 2011, there was much pre-season media speculation over a possible move to new AFL club Greater Western Sydney. This was put to rest during the lead-up week to the season's commencement when Collingwood announced that Swan had signed a new three-year deal, committing him to the club until the end of 2014. Swan started 2011 in the same good form as 2010. He attained 40 disposals in Round 2 against North Melbourne but sustained a quad injury close to the midway point of the season and his form deteriorated. Collingwood decided to send Swan, with team mates Brent Macaffer, Darren Jolly and Nathan Brown, to a high altitude training camp in Arizona in an attempt to help the players recover faster from their individual injuries. The trip proved effective for Swan, with an immediate effect on his playing performances. In the next six games after his return, he had an average of 35.33 disposals per game with a strong effort against Essendon with 45 possessions and one goal. He later won the 2011 Brownlow Medal with 34 votes - the most recorded in a count since the 3-2-1 system came into effect.
Swan received some criticism early on in the 2012 season and was accused of being unfit and "too fat". In the annual Anzac Day clash, Swan won his first Anzac Day medal as best on ground after a one-point win over Essendon, with 42 possessions, three goals and six tackles during the game. Swan missed two games midway through the season due to a hamstring injury, then returned for the Queen's Birthday clash in Round 11 against the Melbourne, where he finished with a game high 42 possessions. Strong performances over the following two months saw Swan rise in the Brownlow Medal betting, to become one of the favourites behind Jobe Watson, Scott Thompson and Gary Ablett Jr. Swan was later found to have broken a pledge made by the playing group to abstain from drinking alcohol for the remainder of the season. He was suspended for two games as a result. Swan had over 40 disposals in 6 different games, reaching a new career high of 49 against Hawthorn in the round 17 loss, he also didn't have below 25 disposals showing how consistent he was. Swan over the home and away season averaged 35.66 disposals (career high and AFL record since stats were recorded) and 1.2 goals a game. Despite missing 4 home and away games Swan still finished 4th on the Brownlow medal count and averaged more votes per game than anyone else in the top 10.
 Swan finished fourth in the Brownlow Medal, and was named on the bench in the All-Australian, his fourth selection in his career.
Swan started the season in usual outstanding fashion, averaging 30 possessions in the first 3. In round 4, Swan played his 200th AFL game against an unbeaten Richmond, producing an almost best on ground performance (35 disposals, 6 marks and 1 goal) and was only bettered by teammate Travis Cloke, who kicked a career best 7 goals. At the end of the year Swan averaged 31.2 disposals, 5.7 marks, 3.4 tackles, and 5.2 inside 50s per game. He finished first in overall disposals, and equal 7th in total inside 50s. Swan was selected as Ruck-Rover in the 2013 All-Australian Team, the fifth consecutive year he has been included. Swan finished third in the Brownlow Medal with 26 votes, losing by two to the winner Gary Ablett, and one to second placed Joel Selwood.
After wrist surgery in the off season, Swan started the season slowly, with an average of 22 disposals in the first 3 rounds, including just 16 disposals in round 2. It didn't take long for him to find his form though, including 35 disposals and 11 marks against North Melbourne, and 26 disposals and 4 goals against Essendon to earn him his 2nd ANZAC medal.
In 2003, Swan was arrested with two others following a brawl at Federation Square in which a security guard was knocked unconscious. Swan was charged with 13 offences, including assault, affray and intentionally causing serious injury. Swan was convicted of affray and ordered to perform 100 hours community service. The victim sued his three assailants and in a settlement, $100,00 was paid by the three offenders. In an interview in 2010, Swan detailed how close the incident came to ending his football career. Coach Mick Malthouse gave him a second chance, believing that Swan did not deserve to have his career derailed because of one stupid decision.
In July 2010, Swan was hit in the mouth at a nightclub.
In August 2012, Swan received an internal two-match suspension from the Collingwood senior team for breaking team rules – specifically, a pledge by the playing group to abstain from alcohol between late July and the end of the season.
In June 2014, Swan attended a fundraising event hosted by John Gatto, the brother of underworld figure Mick Gatto. Collingwood president Eddie McGuire had no problem with the incident.