The 2006–07 season was Villarreal Club de Fútbol's 84th season in existence and the club's 7th consecutive season in the top flight of Spanish football.

In addition to the domestic league, Villarreal participated in this season's editions of the Copa del Rey and the UEFA Intertoto Cup.

The season covered the period from 1 July 2006 to 30 June 2007.

Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.

Players may hold more than one non-FIFA nationality.