Cassidy played with the Toronto Blue Jays (2002), Boston Red Sox (2005) and San Diego Padres (2005–2006).

Cassidy Scott began his MLB career with the Toronto Blue Jays in 2002 appearing in 58 games and logging 66.0 innings.

On April 18, 2004, the Jays traded Cassidy to their AL East rival, the Boston Red Sox, for a player to be named.

Scott did not prove to be a major acquisition as he finished the 2004 campaign playing on the Red Sox's Triple-A affiliate in Pawtucket.

Cassidy signed a minor league contract with the Milwaukee Brewers on December 3, 2007, but announced his retirement on March 2, 2008.