After attending draft camp and showing promise, Hawthorn selected Franklin with their second pick, number five overall, in the 2004 AFL Draft. In a 2012 interview on the Fox Footy program On The Couch, Franklin admitted that his "free spirit" probably scared a few clubs away from selecting him that year. Debuting in Round 1 of the 2005 season against the Sydney Swans at the SCG, he showed a strong presence up forward and played 20 out of 22 games, kicking 27 goals.
After injuring his ankle and hand early in the 2006 season, Franklin made his way back to senior level through the VFL, and played his first AFL game of the season in Round 9 against Sydney. In Round 12, he kicked six goals against Richmond. On July 13, 2006, Franklin signed a two-year deal to remain at Hawthorn after being linked with clubs such as Essendon, Fremantle and the West Coast Eagles. Another six-goal game late in the season prompted predictions of Franklin to be the next big-name forward in the AFL.
In 2007, Franklin finished the home-and-away season with 63 goals, finishing third in the Coleman Medal behind Fremantle captain Matthew Pavlich and the eventual winner, Brisbane Lions co-captain Jonathan Brown. Franklin's tally included a career-high nine goals against Essendon in Round 6. However, in Round 21 against the Western Bulldogs, he kicked eleven behinds with his two goals. Only Richmond's Jack Titus and St Kilda's Dave McNamara have kicked more behinds in a game without managing more than two goals. In the 1st Elimination Final of 2007, the Hawks mounted a big comeback in the second half against the Adelaide Crows. Franklin was instrumental in the win, kicking seven goals in his finals debut, including the match-winning goal from outside 50 metres with seven seconds remaining in the match. Hawthorn were eliminated from the finals the following week by North Melbourne.
Franklin finished the season with an equal-third finish in Hawthorn's best-and-fairest award, the Peter Crimmins Medal, and was Hawthorn's leading goalkicker for the first time in his career.
Thousands of supporters take to the field after Franklin kicked his 100th goal for the 2008 season, in Round 22 against Carlton
2008 saw Franklin establish himself as one of the elite players in the competition in what proved to be his career-best season, and he won his first Coleman Medal with 102 goals in the home-and-away season. His season-high haul of nine goals came once again against Essendon in Round 11. He also played for the Dream Team in the AFL Hall of Fame Tribute Match, kicking four goals.
Franklin kicked his 100th goal for the home-and-away season against Carlton in Round 22 at Etihad Stadium, becoming the first player to kick 100 goals in a season since Tony Lockett in 1998, and the first Hawthorn player since Jason Dunstall in 1996. Upon reaching the milestone, thousands of supporters stormed the field and formed a large huddle around Franklin, who was promptly ushered from the field and into the change rooms until the supporters had cleared. Prior to the match, the AFL had warned of a $6000 fine for every person who jumped the fence. He also was the first player of Aboriginal descent to achieve this. He then added to his tally by kicking another eight goals in the qualifying final against the Western Bulldogs, tying with Dermott Brereton for the most goals kicked by a Hawthorn player in a finals match. He kicked just one goal against St Kilda in the preliminary final, before Hawthorn went on to win the premiership. Although Franklin did not play a large part in the grand final, his two goals brought his season tally up to 113 goals. Franklin was named as full forward in the All-Australian Team that year, his first ever selection; he then received his first Peter Crimmins Medal for his outstanding season.
Franklin’s a physical freak. He’s probably the player I most enjoy going to watch.
Franklin missed the 2009 NAB Cup after undergoing surgery on his thumb and his shoulder in the off-season. On his return to senior football, his form fell well short of his 2008 performances. He played his 100th game in Round 19 against St Kilda at Hawthorn's second home, Aurora Stadium in Launceston, Tasmania. During the game, one of Franklin's teeth fell out during a marking contest with Saints defender Zac Dawson.
In Round 21, Franklin was suspended for two matches as a result of a hip-and-shoulder against Richmond midfielder Ben Cousins. The Hawks appealed the decision, but failed. As a result, Franklin missed Hawthorn's final home-and-away match against Essendon, which the Hawks lost, and they therefore missed out the finals, causing Franklin to miss Round 1 of the following season.
Franklin missed three of the first seven matches of 2010, all through suspension, as Hawthorn lost six matches in succession after Round 1. However, Franklin was back to his best form in Round 9 against Carlton at Etihad Stadium, when he led Hawthorn to a 50-point win with five goals. He showed glimpses of his 2008 form and looked to have his goalkicking form back, as he was back to his career average of more than three goals a game (324 goals in 106 games after Round 9). However, in Round 10, Franklin was suspended for the third time in eight matches for a head-high bump on Sydney Swans' defender Martin Mattner.
In Round 13, Franklin effectively dragged Hawthorn over the line for a win against their arch-rival in Essendon. He kicked five goals for the match, but his last two were the standouts - the final one in particular, a goal from the boundary line on a tight angle after having run from half-back, which was later chosen as Goal of the Year. Franklin kicked five goals in Round 17 against St Kilda after returning from an ankle injury; despite his performance, the Saints forced a draw during the final seconds of the match. In Round 22, Franklin kicked six goals against Collingwood, helping the Hawks clinch a three-point come-from-behind victory against the eventual premiers. It was the first time that he had kicked more than five goals since 2008. Frankin was again named in the All-Australian team that year.
After a moderately good year in 2010, Franklin had a consistent start to the 2011 season. In Round 8 against the Sydney Swans at the SCG, Franklin kicked his 400th goal for Hawthorn in a six-goal outing as the Hawks beat the Swans by 46 points. He continued his consistent goalkicking form for the remainder of the year, including a season-high eight goals in a club-record 165-point win against a young Port Adelaide side at the MCG in Round 21. Franklin went on to win his second Coleman Medal that year with 71 goals, despite spending a significant amount of time further up the ground.
Franklin was Hawthorn's sole target up forward in their qualifying final loss to the Geelong Cats, kicking four goals. However, in the fourth quarter, he landed heavily in a marking contest and hyperextended his knee. While footage of the incident suggested possible damage to his anterior cruciate ligament, scans later revealed that he had instead suffered bone bruising and bleeding; nevertheless, most observers considered Franklin's season to be over following the loss. However, he returned the following week against the Sydney Swans, kicking another four goals and playing an important part in the Hawks' eventual win. Despite spending time in hospital with a virus in the lead-up to the preliminary final against Collingwood, Franklin was a constant danger throughout the match. He kicked three goals, including a dribble kick in the forward pocket from a tight angle, which almost sealed victory for Hawthorn until Collingwood kicked a late goal and won the match, eliminating the Hawks. Franklin was named at full forward in the All-Australian team for the second time in his career for his consistent season.
Franklin struggled early in the season with inaccurate goalkicking, kicking 21 goals and 36 behinds in his first nine matches. However, he dramatically reversed his fortunes in Round 10 when he kicked a career-high 13 goals in a 115-point drubbing of North Melbourne at Aurora Stadium. Franklin was also among one of the five players that year to reach the milestone of 500 career goals, which occurred in a 162-point demolition of newcomers Greater Western Sydney in Round 15, nearly eclipsing the club-record winning margin set the year before. He is the second indigenous player to reach 500 goals, the fifth Hawthorn player, the seventh-youngest and the tenth-quickest from debut. However, Franklin suffered a hamstring injury the week before and continued to play, before injuring it further in the Giants game which, along with an illness, caused him to miss six matches.
Franklin returned against the Sydney Swans at the SCG in Round 22, kicking four goals in a seven-point come-from-behind victory against the eventual premiers, including three in the second quarter. Franklin played a minor role in the finals series that year, but kicked a goal late in the last quarter of the preliminary final against the Adelaide Crows which sealed the game for the Hawks, allowing them to qualify for the Grand Final against the Sydney Swans, where Franklin kicked three goals in a losing side.
Before the start of the 2013 season, Franklin, who was in the final year of his four-year contract with Hawthorn at the time, announced that he would not begin talks with Hawthorn about a new contract until the end of the season. Having played for nine seasons at Hawthorn, he was classified as a restricted free agent at the end of the season, meaning that the club could retain Franklin if it was able to match any rival offers.Greater Western Sydney was considered the most likely destination if Franklin was to choose to leave Hawthorn.
Franklin kicked 60 goals during the 2013 season, the first time since 2006 that he had kicked less than three goals per game, as he became less of a focal point in the Hawthorn forward line, while teammate Jarryd Roughead enjoyed a career-best season with 72 goals, earning him the Coleman Medal. However, a leap and goal on the run in Round 3 against Collingwood earned Franklin his second Goal of the Year. Franklin played in the 2013 AFL Grand Final in which Hawthorn defeated Fremantle; this was the second time that he had played in a Hawthorn premiership winning side. Despite this, his season was dominated by media speculation over his contract situation, and playing in a second premiership at Hawthorn only strengthened rumours of his impending departure, with many believing that he was set to finish his career at Hawthorn on a high note.
After months of speculation dating back to before the start of the season, on October 1, 2013, Greater Western Sydney shocked the football public by withdrawing their offer of $1.2 million per year for six years, announcing that they were of the belief that Franklin was set to sign with the Sydney Swans. The Sydney Swans' chairman, Andrew Ireland, said later that day that the contract offered to Franklin was a nine-year deal worth $10 million, and that Franklin's management first approached the Swans about the move shortly after the 2012 AFL Grand Final, when Franklin played in a losing side against the Swans. The next day, Franklin said that he did not make his decision to move to Sydney "until the last minute". He also said, "I'm looking forward to getting up to Sydney. It's a great footy club and, as I said, I had to pack my bags up at Hawthorn and saying goodbye to the boys is something very tough, and upsetting, too". Franklin's manager, Liam Pickering, also revealed that the nine-year contract was so back-ended that he would be making less money with the Swans in 2014–15 than he was at Hawthorn in 2013.
Franklin officially joined the Sydney Swans on October 8, 2013, a week after the move was first announced, after Hawthorn decided against matching the offer made to the restricted free agent. The next day, Franklin was unveiled by the Swans at the SCG. Later in October, Franklin travelled to Ireland with the Australian International Rules team for the 2013 International Rules Series. It was the first time that Franklin had represented Australia in international rules football, and he managed one over in the first match of the two-test series. Following the first match, he travelled back to Australia for the wedding of his former teammate Brent Guerra, and was unable to participate in the second test.
Prior to the 2014 season, his first as a Swan, Franklin opted to continue wearing the no. 23 guernsey that he previously wore for Hawthorn. He made his debut for the Sydney Swans in Round 1 in the Sydney Derby against cross-town rivals Greater Western Sydney at Giants Stadium, and finished the game with one goal in a shock loss. After a slow start for both Franklin and the Swans, when they lost three of their first four matches, Franklin returned to form against Fremantle at the SCG, kicking four second-half goals in what would be the first of a club-record-equaling 12 successive wins, during which he twice narrowly avoided suspension. In Round 8 against Hawthorn at ANZ Stadium, Franklin kicked seven successive behinds in the first three quarters, before kicking two fourth-quarter goals to seal an upset victory in Franklin's first match against his former side.
Franklin continued his outstanding form throughout the season (despite kicking 2.7 and 3.5 in two matches against his former side in Hawthorn) and went on to win his third Coleman Medal, kicking 67 goals in 19 matches during the home-and-away season. Franklin was selected at full forward in the All-Australian team for the third time in his career for his outstanding season; he then went on to finish equal-second in the 2014 Brownlow Medal count on a career-high 22 votes (the most votes ever polled by a Coleman Medallist), beating the tally of 20 votes he achieved in his other Coleman Medal-winning years of 2008 and 2011. Franklin was one of the Swans' best players throughout the finals series, including a four-goal performance in the Swans' losing grand final to Hawthorn - his highest ever tally in a grand final.
Franklin began the 2015 season with a solid three-goal performance against Essendon at ANZ Stadium, improving his record against the Bombers to 58 goals in 12 games. His best game was in round 9 against Carlton at the SCG, when he kicked seven goals. He would finish the year with 47 goals from 17 games, missing four of the last seven games due to a back injury. It was the first time since 2006 that he had kicked less than 50 goals in a season. He then withdrew from playing in the 2015 AFL finals series due to a mental illness.