Mokoena made his debut for Blackburn on 8 January 2005 in an FA Cup match against Cardiff City, coming on as a 43rd-minute substitute for Barry Ferguson.

From then on, Mokoena found himself used sparingly as a holding midfielder in his favoured 4–5–1 formation as a second-half substitute, charged with protecting leads in games in which Blackburn were winning.

With Robbie Savage out injured for Rovers, Mokoena started most of the team's games in 2007 and he scored his first goal for Blackburn in an FA Cup 6th round victory against Manchester City on 11 March 2007.

[5] He scored his first goal for Portsmouth in the last minute of extra time to give them victory over Coventry City at the Ricoh Arena in the dying seconds in the FA Cup third round replay on 12 January 2010.

Mokoena played a major part in the games against Coventry, Sunderland, South Coast rivals Southampton, Birmingham and Tottenham.

[6] He stated that he desired the move to secure regular football, especially in the run up to the 2010 World Cup held in South Africa his native.

[8] Following Portsmouth going into administration in February 2012 and the club's subsequent relegation into the third-tier Football League One, Mokoena was identified a potential key player to leave due to his relatively high salary.

He is the youngest ever player to have represented South Africa,[12] having played in 1999 for the 2000 Summer Olympics qualifiers aged 18–19; he later replaced Lucas Radebe as captain of his country.