From 2001-2003, the first three years of his career, Duckworth pitched with the Philadelphia Phillies, compiling a 15-18 record. While with the Phillies, Duckworth had a fan section called the Duck Pond. On November 3, 2003, he was traded by the Philadelphia Phillies with minor leaguer Taylor Buchholz and Ezequiel Astacio to the Houston Astros for Billy Wagner. Spending the next two years in Houston with limited playing time, Duckworth signed as a free agent with the Pittsburgh Pirates in December 2005.
Without wearing a Pirates uniform in 2006, he was traded by Pittsburgh to the Kansas City Royals for cash considerations. In his first two seasons with the Royals, his record was 4-10 with a 5.37 ERA.
In January 2008, Duckworth was designated for assignment by the Royals to make room on the organizational roster for free agent signee Brett Tomko. He passed through waivers, and on February 1, the Royals announced that Duckworth had accepted an assignment to Triple-A Omaha. On August 24, 2008, he was recalled by Kansas City to start; in his first game, he went 5 innings, giving up 3 earned runs, and was credited with the win. In October 2009, Duckworth was granted free agency.
In January 2010, Duckworth signed a minor league contract to play with the Philadelphia Phillies organization.
In December 2010, Duckworth signed a minor league contract with the Boston Red Sox.