Anderson began his coaching career in 1999 at the Parramatta Eels working his way up to Premier League coach before being made assistant coach to Brian Smith in 2000.
New Zealand Warriors
In 2001, Anderson was a surprise choice for coach of the New Zealand Warriors. He had amazing success, taking them to their first finals series in 2001 and their first Grand Final in 2002, losing to the Sydney Roosters. The 2002 Dally MCoach of the Year was awarded to Anderson. He took the Warriors to another Finals series in 2003, the same year he replaced Gary Freeman as head coach of the New Zealand national rugby league team. Anderson resigned from the Warriors in June 2004 after a bad start to the season; winning only three out of eleven games. Anderson retained his position as coach of the New Zealand Kiwis until June 2005.
On 17 November 2008 Anderson was announced the head coach of the Parramatta Eels NRL squad for three years, beginning in 2009. He guided the Eels to a remarkable 2009 National Rugby League Grand Final from a position where after 18 rounds the Eels were tipped 150/1 to win the NRL. On 25 September 2010, it was announced that Anderson's contract had been terminated with immediate effect by the club, who replaced him with Stephen Kearney. On 18 October 2013, it was announced that Anderson would leave his post as NRL Referees elite performance manager to return to Parramatta in the newly created job as general manager of football operations. In 2014, a report revealed that a review was conducted in order to determine whether Anderson should have been granted a contract extension as head coach back in 2011. Anderson "had suggested his position would be untenable for the 2011 season and the level of undermining and the resultant instability would make his job impossible", the report read. "He was very disappointed and it was going to be a long year for all. He claimed his staff were ‘not on his bus’ and that it was a toxic environment". The report also alleged that players had turned up to recovery sessions intoxicated or smelling of alcohol and that "he also struggled to handle relationships that longer serving staff and players had with the board." In 2016, Anderson along with four other board members were de-registered by The NRL and had their contracts terminated by Parramatta in the wake of the club's salary cap scandal. It was alleged that Anderson along with the other board members which the media dubbed "The gang of five" had been aware of or made payments to players outside of the game's rules. If found guilty of this, Anderson could face a maximum sentence of 10 years in jail for fraud.
Sydney Roosters
On 30 January 2019, it was revealed that Anderson had joined the Sydney Roosters in a recruitment role. Before Anderson was allowed to join the club, the Eastern Suburbs outfit had to convince the NRL that he was a fit and proper person befitting registration. An NRL spokesman said Anderson had been approved to join Easts with some restrictions on his role after two years out of the game.
Honours
Dally M Coach of the Year2002 NRL Grand Finalist2002, 2009 Challenge Cup Winner2006, 2007, 2008 Super League Grand Final Winner2006 BBC Coach of the Year2006 World Club Challenge Winner2007