Carr was traded to Fremantle at the 2000 AFL Draft by St Kilda in exchange for Craig Callaghan. He played 21 games in Fremantle's disastrous 2001 season, which saw the club take out the wooden spoon; having been part of the St Kilda side that finished last in 2000, this meant Carr played in consecutive wooden spoon seasons with two different sides. He played every game in 2002 and after an excellent 2003 season, in which he was sixth in Fremantle's best and fairest, his 2004 season was severely disrupted by injury. An ankle problem early in the season and a broken leg later in the season saw Carr restricted to just 11 games.