His first-grade debut was for the South Sydney Rabbitohs against the New Zealand Warriors at Ericsson Stadium in round 9 of the 2002 NRL season, scoring a try on debut.
At the end of the 2003 season Merritt agreed to terms with the Cronulla Sharks where he was to play for the next two years.
In the 2005 season, Merritt endured a tough year.
He played only three first grade games for the Sharks, but was a stand-out player in the lower grade NSWRL Premier League matches for the Newtown Jets, scoring almost 300 points for the year.

In one game against the Windsor Wolves, he scored 40 points (including 5 tries).
At the end of the season, Merritt picked up a number of awards including Newtown RLFC VB Premier League Players' Player award, as well as having the distinction of being the Jets highest season point scorer, as well as most points in a game.

(as of 2005).
His outstanding showing that year was rewarded when his old club South Sydney offered him a two-year contract to play in the NRL.

For the 2006 NRL season, Merritt rejoined the Rabbitohs and was a standout performer in an underachieving side all year, being one of only three players to play all 24 games for the club.
He was the highest try scorer for the 2006 season with 22 tries, beating Manly Sea Eagles' fullback Brett Stewart who scored 20.
It was the first time since Nathan Blacklock in 2000 that the leading try scorer in a season played for a club that missed the finals, and the first time in Australian rugby league history that the leading try scorer in a season played for the club that finished last on the competition ladder.
 Notably, in the first three rounds of the season Merritt scored a try in the final minute of each game, a feat that had never been achieved in three consecutive games.
Nathan's hard work and great performances through the year culminated in the announcement that he had earned his first representative honor, to play for the Prime Minister's XIII on their annual end of season tour to Papua New Guinea, the only South Sydney player to make in the squad.
The Australians beat the Papua New Guinea Kumuls 28–8, with Merritt one of the try-scorers.
He was also included in the train-on squad for the Kangaroos squad for the 2006 Tri-Nations tournament against England and New Zealand, but missed out on a starting position.

Following the announcement of the City Origin squad in 2007, Merritt hinted that his non-selection was possibly due to "a Souths thing or a racial thing".
This comment was lambasted and in rebuttal to this comment critics pointed to the selection of Parramatta's Jarryd Hayne (Fiji) and Canterbury-Bankstown's Hazem El Masri (Lebanon) as evidence that selections had not been racially motivated.
The Rabbitohs eventually made the finals for the first time since 1989 but Merritt was injured in the second-last round of the competition so was unable to play in the match they ultimately lost to Manly-Warringah.

Merritt scored a hat-trick to begin the 2009 season against the Roosters in a match the Rabbitohs won 52–12.
In round 10 Merritt was responsible for one of the most iconic moments in modern rugby league.
With less than 10 seconds left in the Heritage Round match against the Wests Tigers at the Rugby League's spiritual home of the SCG he kicked a field goal to win the game for the Rabbitohs, 23–22.
This was the only field goal he ever kicked in his career.
The fact the Rabbitohs came from 12 points behind late in the game, it was Heritage Round, the game was at the SCG, it was in the final moments in the game and he had never kicked a field goal all contributed to the aura surrounding this moment and the legacy it has produced.
At the 2009 Dally M Awards, he was awarded the Peter Frilingos Memorial Award for Headline Moment of the Year for the field goal.

Merritt's great experiences at the SCG continued in 2010 when he scored a hat-trick, once again against the Wests Tigers in Heritage Round.
His first-grade debut was for the South Sydney Rabbitohs against the New Zealand Warriors at Ericsson Stadium in round 9 of the 2002 NRL season, scoring a try on debut. At the end of the 2003 season Merritt agreed to terms with the Cronulla Sharks where he was to play for the next two years. In the 2005 season, Merritt endured a tough year. He played only three first grade games for the Sharks, but was a stand-out player in the lower grade NSWRL Premier League matches for the Newtown Jets, scoring almost 300 points for the year. 
In one game against the Windsor Wolves, he scored 40 points (including 5 tries). At the end of the season, Merritt picked up a number of awards including Newtown RLFC VB Premier League Players' Player award, as well as having the distinction of being the Jets highest season point scorer, as well as most points in a game. 
(as of 2005). His outstanding showing that year was rewarded when his old club South Sydney offered him a two-year contract to play in the NRL.
For the 2006 NRL season, Merritt rejoined the Rabbitohs and was a standout performer in an underachieving side all year, being one of only three players to play all 24 games for the club. He was the highest try scorer for the 2006 season with 22 tries, beating Manly Sea Eagles' fullback Brett Stewart who scored 20. It was the first time since Nathan Blacklock in 2000 that the leading try scorer in a season played for a club that missed the finals, and the first time in Australian rugby league history that the leading try scorer in a season played for the club that finished last on the competition ladder.  Notably, in the first three rounds of the season Merritt scored a try in the final minute of each game, a feat that had never been achieved in three consecutive games. Nathan's hard work and great performances through the year culminated in the announcement that he had earned his first representative honor, to play for the Prime Minister's XIII on their annual end of season tour to Papua New Guinea, the only South Sydney player to make in the squad. The Australians beat the Papua New Guinea Kumuls 28–8, with Merritt one of the try-scorers. He was also included in the train-on squad for the Kangaroos squad for the 2006 Tri-Nations tournament against England and New Zealand, but missed out on a starting position. 
Following the announcement of the City Origin squad in 2007, Merritt hinted that his non-selection was possibly due to "a Souths thing or a racial thing". This comment was lambasted and in rebuttal to this comment critics pointed to the selection of Parramatta's Jarryd Hayne (Fiji) and Canterbury-Bankstown's Hazem El Masri (Lebanon) as evidence that selections had not been racially motivated. The Rabbitohs eventually made the finals for the first time since 1989 but Merritt was injured in the second-last round of the competition so was unable to play in the match they ultimately lost to Manly-Warringah.
Merritt scored a hat-trick to begin the 2009 season against the Roosters in a match the Rabbitohs won 52–12. In round 10 Merritt was responsible for one of the most iconic moments in modern rugby league. With less than 10 seconds left in the Heritage Round match against the Wests Tigers at the Rugby League's spiritual home of the SCG he kicked a field goal to win the game for the Rabbitohs, 23–22. This was the only field goal he ever kicked in his career. The fact the Rabbitohs came from 12 points behind late in the game, it was Heritage Round, the game was at the SCG, it was in the final moments in the game and he had never kicked a field goal all contributed to the aura surrounding this moment and the legacy it has produced. At the 2009 Dally M Awards, he was awarded the Peter Frilingos Memorial Award for Headline Moment of the Year for the field goal.
Merritt's great experiences at the SCG continued in 2010 when he scored a hat-trick, once again against the Wests Tigers in Heritage Round.
Nathan Merritt