Blackburn survived that season but again struggled in the 2004–05 season, not winning a game until September 2004. However, the club preserved their Premiership status following a change of manager and reached the FA Cup semi-finals, where they lost to Arsenal. Emerton paid credit to new manager, Mark Hughes, ""It is a huge achievement. When Mark came in we were in a bit of disarray but from the day he arrived we worked on our fitness. Everyone is better for that and it has shown in our performances."
A more successful season in 2005-06 saw Blackburn reach the 5th round of the FA Cup, losing to West Ham, the semi-finals of the Carling Cup, losing to Manchester United, and qualify for the UEFA Cup. Following the end of the season, Emerton signed a new four-year deal at Blackburn in August 2006. Mark Hughes described him as "...a player who gives me a lot of options. He can carry the ball from one end of the field to the other. That's why teams have coveted him this summer." Emerton made 47 appearances in the 2006-07 season as Blackburn finished in mid-table but reached the FA Cup semi-final for the second time in three years, losing to Chelsea, and reached the knock-out stages of the UEFA cup, eventually losing out to Bayer Leverkusen for a place in the last 16. At the end of the 2006-07 season, Emerton had made a total of 167 appearances for Blackburn in all competitions, scoring 10 goals.
In July 2008, Emerton signed a new four-year contract, to keep him at the club until summer 2012.
Emerton played in both legs of World Cup play-off against Uruguay in November 2005, when the Socceroos qualified for the 2006 FIFA World Cup in Germany, the first time that Australia had reached the finals of the World Cup since 1974, and was named in the Australian squad for the World Cup finals. He was in the starting lineup for all three Group Stage games against Japan, Brazil and Croatia as Australia qualified for the second round. However, he received two yellow cards against Croatia, was sent off in the 87th minute and subsequently missed the Socceroos' second round match against Italy.
Emerton scored 2 goals against Qatar in Australia's 4th match of World Cup Qualification for the 2010 FIFA World Cup, in Doha Qatar. The match finished 3-1 to the Australians, with former Liverpool FC striker Harry Kewell getting Australias 3rd goal, and consequently Harry's 2nd of the tournement, as well as Australia advancing to the 2nd round of the World Cup.
| Club | Season | League | Cup * | Europe | Total | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Apps | Goals | Assists | Apps | Goals | Assists | Apps | Goals | Assists | Apps | Goals | Assists | ||
| Feyenoord Rotterdam | 2001–02 | 25 | 6 | - | - | - | - | 7 | 0 | - | 32 | 6 | - |
| 2002–03 | 33 | 3 | - | - | - | - | 9 | 0 | - | 41 | 3 | - | |
| Blackburn Rovers | 2003–04 | 37 | 2 | 12 | 1 | 0 | - | 2 | 1 | - | 40 | 3 | 12 |
| 2004–05 | 37 | 4 | 4 | 7 | 1 | - | 0 | 0 | 0 | 44 | 5 | 4 | |
| 2005–06 | 30 | 1 | 3 | 7 | 1 | - | 0 | 0 | 0 | 37 | 2 | 3 | |
| 2006–07 | 34 | 0 | 3 | 7 | 0 | 1 | 6 | 0 | 0 | 47 | 0 | 4 | |
| 2007–08 | 30 | 1 | 0 | 3 | 0 | 0 | 4 | 0 | 0 | 37 | 1 | 0 | |
| Career totals | 245 | 20 | 23 | ||||||||||