Selwood was recruited from Bendigo Pioneers as the West Coast Eagles' third pick, and number 53 overall in the 2002 AFL Draft. In 2003, his debut season, Selwood played two games including the losing elimination final against Adelaide. He played three games in 2004 before osteitis pubis curtailed his season.
In 2005, Selwood played 21 matches and received a rising star nomination in round 16. He was knocked unconscious in a collision with Adelaide captain Mark Ricciuto in round 22 but the forced layoff helped Selwood to recover from compartment syndrome. He returned in the preliminary final against Adelaide and played in the grand final against Sydney, which the Eagles lost by four points.
2006 saw him cement his place in the Eagles' starting 22, and build a reputation as a defensive midfielder. Selwood played in all of the 26 games for West Coast in 2006.
Selwood finished third in West Coast's club champion awards in both 2007 and 2008. He played all 22 games in 2008 and was a vice captain of the Australian team that played Ireland in the International Rules series.
On 14 April 2007, Selwood was involved in an altercation with Fremantle's Des Headland. Both appeared before the AFL Tribunal on 18 April. Headland was charged with two counts of striking Selwood, and one count of wrestling with him, while Selwood was charged with using insulting language towards Headland. On 18 April, the tribunal found Selwood not guilty of using insulting language. It found Headland guilty of two of the three charges but elected not to impose a penalty.