2001 Bowen made his NRL debut in Round 1 of the
2001 NRL season against
Queensland rivals, the
Brisbane Broncos, coming off the bench in his side's 17–18 loss at
Dairy Farmers Stadium. He scored his first NRL try in Round 9 against the
Canberra Raiders, coming off the bench again in a 26–34 loss. In his rookie season, Bowen played 15 games, scoring six tries and kicking one goal. After spending time on the bench and at five-eighth, Bowen played his primary position of fullback for the final seven games of the season. At the end of the season Bowen was selected at halfback for the
Junior Kangaroos, alongside future Cowboys teammates
Dallas Johnson,
Micheal Luck and
Brent Tate.
2002 Despite finishing 2001 as the club's starting fullback, Bowen vacated the role at the start of the
2002 NRL season for the returning
Tim Brasher, who was the Cowboys' captain at the time. Bowen played on the wing in Round 1, in a game where Brasher would once again succumb to injury, vacating the fullback spot. In Round 2, Bowen played five-eighth in the Cowboys' loss to the Broncos before taking over the fullback position permanently a week later. Bowen enjoyed a breakout season in 2002, scoring 12 tries in 24 games, including a run of five games in which he scored a try.
2003 In 2003, Bowen made his representative debut, being called up to the
Queensland team for Game II of the
State of Origin series. He played 16 minutes as a substitute, as Queensland lost the series. He was selected again for Game III of the series, coming off the bench in Queensland's 36–6 win. Bowen played 20 NRL games in 2003, scoring nine tries, including his first NRL
hat-trick in the Cowboys' 60–8 win over the
South Sydney Rabbitohs in Round 24.
2004 The Cowboys made the finals series for the first time in
2004, with Bowen playing a key role in the side which finished one match short of their first Grand Final. In 23 games, he scored 11 tries, including one in the Cowboys first ever finals game, a 30–22 victory over the
Canterbury Bulldogs. Bowen once again represented Queensland in 2004, playing in all three
games and scoring his first Origin try in the Maroons' Game III loss. At the end of the season Bowen was selected in the
Australian Kangaroos squad for the
Tri-Nations series. He played at fullback in a tour match against
Cumbria, scoring a try, although he did not play in the Tri-Nations series, with
Anthony Minichiello preferred as the Kangaroos' fullback. However, after the Tri-Nations series, he made his Test debut in a one-off match against
France in
Carcassonne, that Australia won 52–30. On the touring squad's return journey to Australia, he scored three tries in a non-Test exhibition match against the
United States in
Philadelphia.
2005 In 2005, halfback
Johnathan Thurston joined the Cowboys, in what would prove to have a major effect on not just the club but on Bowen's career. Over the next nine seasons, Bowen and Thurston would form one of the competition's most dangerous combinations. On the back of Thurston and Bowen, the Cowboys made it to the
2005 NRL Grand Final, the club's first. Despite Bowen scoring the opening try, they lost to the
Wests Tigers, 30–16. Bowen's 21 tries in 2005 made him the competition's top try scorer. Bowen was again selected for Queensland in the
2005 State of Origin series. In Game I of the series, he proved to be the game-breaker. After coming off the bench in the second half, he intercepted a pass from New South Wales half-back
Brett Kimmorley and ran 40m to score in
golden point extra time, thus winning the game for Queensland. Bowen would also score tries in the second and third games of the series, although Queensland lost both matches to lose the series. He was selected in Queensland's starting line-up in the third match for the first time in his career, displacing
Billy Slater.
2006 In
2006, Bowen and the Cowboys failed to capitalise on their progress from the previous season, finishing ninth on the ladder and missing the finals series. Bowen played Game I of the
2006 State of Origin series but was dropped from Queensland's side for Game II. He scored just five tries in 24 matches for the Cowboys, one of the lowest season tallies of his career.
2007 In 2007, Bowen enjoyed his most successful individual season. He regained his top try scorer's title, with 22 tries, and also made the most line breaks (32) and tackle breaks (220) in the NRL. He returned to the Queensland squad for Game III of the
State of Origin series, and the Cowboys returned to the NRL finals, finishing third on the ladder. He was voted by his peers as the Rugby League Player Association's Player of the Year, was named the Cowboys' Player of the Year for the first and only time in his career, was named
Rugby League Week Player of the Year and was named Fullback of the Year at the
2007 Dally M Awards. He also signed a new contract to remain at the Cowboys through the 2011 season, with his coach
Graham Murray claiming he was the "best fullback in the game". Despite the accolades for his performances during the year, Bowen was controversially omitted from the Kangaroos side to face New Zealand at the end of the season, as
Brett Stewart and
Kurt Gidley were preferred at fullback. Kangaroos' coach
Ricky Stuart argued that Bowen's small stature was a factor against his selection. Former dual-code international
Wendell Sailor argued that selectors were correct to leave Bowen out of the national team, suggesting that his form in club football had not been replicated at State of Origin level.
2008 Bowen started the
2008 NRL season slowly, missing Rounds 4 and 5 due to a left knee injury. He returned in Round 6 against the
Warriors and scored three tries. However, three weeks later, Bowen injured his knee again and underwent surgery that ruled him out of action for the rest of the season. Without him, North Queensland finished 15th on the NRL ladder.
2009 Bowen returned from his knee injury in the 2009 pre-season. He scored 12 tries in 20 games before he injured his right knee in August in the same way that he had injured his left knee the previous season. Another round of surgery followed, ruling him out for the remainder of the season and the beginning of the next.
2010 The Cowboys endured a disastrous
2010 NRL season, finishing 15th on the ladder. Bowen missed half the season due to the knee reconstruction he had in 2009, making his NRL return in the Cowboys' Round 9 win over the
Sydney Roosters. Four months later, Bowen played his 200th match for the Cowboys, in their Round 26 loss to the
Roosters. Bowen ended the 2010 season with a career low of two tries. Despite the poor season, Bowen was selected in the
Prime Minister's XIII side that faced
Papua New Guinea in
Port Moresby.
2011 The
2011 NRL season saw Bowen return to his best form, scoring 8 tries in 25 games. He reached another milestone early in the season, surpassing former teammate
Paul Bowman's record for the most NRL games by a Cowboys player. The Cowboys had an improved season, finishing seventh on the ladder and returning to the finals series. At the end of the season, Bowen was once again selected for the Prime Minister's XIII side. During the season, Bowen signed a new contract with the Cowboys through 2013, citing his "love" for the club and a desire to continue to be close to his extended family. He had considered competing offers to play in England. After the season, he was shortlisted for the
Rugby League International Federation's Fullback of the Year award.
2012 During the
2012 NRL season Bowen surpassed the 250 game mark in the Cowboys first home elimination final since 2007, in which they defeated the Broncos 33–16. He recorded 28 try assists in 2012, more than the team's halfback Johnathan Thurston (25), and was 18th man for Queensland in Game III of the
2012 State of Origin series. At the end of the season, Bowen came second in the Dally M Medal tally with 26 points and was a finalist for Dally M Fullback of the Year. He finished 2012 with 13 tries, his most in a season since 2007.
2013 The
2013 NRL season would be Bowen's last with the Cowboys. On 30 August Bowen announced he would be leaving the club at the end of the season. In his final NRL season, Bowen played 19 games and scored six tries. In Round 26, Bowen played his final home game at
1300SMILES Stadium. He was chaired from the field by his teammates after his team's 50–22 victory over the
Wests Tigers, in which Bowen scored two tries. He played his final NRL game a week later in the Cowboys' elimination final loss to the
Cronulla Sharks at
Allianz Stadium. Bowen later said, "I was told I wasn't needed at the club at the time. You get called into the office and they say they haven't got room for you next year … I didn't know what to say …Two years later they won the comp and I would have been a part of it. It was a kick in the guts. Obviously I did so much for this club and my missus is still bitter about it today." On 24 September, the
Wigan Warriors announced the signing of Bowen for the 2014 season as a replacement for departing fullback
Sam Tomkins. in 2014
2014 Bowen's first match for
Wigan was at home against
Huddersfield in Round 1 of the
2014 Super League season, which Wigan lost 8-24. Two weeks later, Bowen returned to Australia and played in Wigan's 14-36
World Club Challenge loss to the
Sydney Roosters. Despite a questionable start to his Wigan career, Bowen ended his first season in England with 15 tries from 24 games, including a hat-trick against the
Hunslet Hawks in the
Challenge Cup. On 16 July, Bowen re-signed with Wigan until the end of 2015. Wigan reached the
2014 Super League Grand Final and Bowen played at fullback in their loss to
St Helens at
Old Trafford.
2015 Bowen began the
2015 Super League season as Wigan's first choice fullback. Two weeks later, Bowen faced his former club's old rivals the
Brisbane Broncos for the final time, in Wigan's 12-14
World Club Series loss. On 7 July, Wigan announced that Bowen would not be offered and new contract. Bowen took over Wigan's goalkicking duties towards the end of the season, kicking 31 goals and scoring 9 tries in his final season. Bowen's final match was the
2015 Super League Grand Final, in which he scored a try and kicked four goals in Wigan's 20–22 loss to the
Leeds Rhinos at
Old Trafford, meaning that he ended his career with a third Grand Final defeat.
2016 Bowen participated in the 2016
NRL Auckland Nines Tournament, returning for the North Queensland Cowboys as a final farewell to the club and his playing career. Bowen would later go on to sign with the
Townsville Blackhawks in Round 11 of the
Intrust Super Cup, debuting for the club in Round 12. He would receive man of the match honours in the Blackhawks 32–12 victory over the
Norths Devils in Round 13, scoring a try and setting up another two. ==Achievements and accolades==