During the 2000 season, the Cubs converted Duncan to relief pitching. Although Duncan said it "took a little bit of getting used to pitching on back-to-back days,"[1] he finished the year with the second-most saves in the Southern League.[6]
Duncan made the final cuts for the Cubs' Major League roster during spring training in 2001 but he was not guaranteed to make the Opening Day roster after the Cubs traded for pitcher Manny Aybar in late March.[7] Duncan was named to the roster for Opening Day, however, after an injury to Tom Gordon; manager Don Baylor waited until after April Fools' Day to inform Duncan.[8] He made his Major League debut on Opening Day, April 2, 2001, at Wrigley Field. He entered in relief of Félix Heredia and threw a nine-pitch walk to Orlando Cabrera of the Montreal Expos.[9] On May 1, he was demoted to Triple-A after Gordon returned from injury. However, a day later, Cubs president Andy MacPhail called him to tell him he was being recalled to the Cubs because pitcher Mike Fyhrie had suffered a broken arm.[10] On May 5, he drew a bases loaded walk against José Núñez and later scored on an error by Dave Hansen; these would be the only run and run batted in of his Major League career.[11][12] Duncan was placed on the disabled list on June 29 after injuring his back while fielding a bunt.[13] He was activated from the disabled list on July 16 and replaced an injured Rondell White on Chicago's roster.[14] Duncan was placed on the disabled list again on July 26 after being diagnosed with tendinitis in his shoulder.[15] Duncan returned from the disabled list on September 1[16] and allowed ten earned runs in his final seven innings pitched of the season.[17]
Heading into the 2002 season, the Chicago Tribune reported that the Cubs were "content with their returning relievers" including Duncan[18] and that he was favored to make the Major League bullpen out of spring training.[19] In spite of that, he was unable to match his 2001 velocity during spring training[20] and began the season in Triple-A Iowa.[21] Duncan was not promoted to the majors again until May 25 following an injury to pitcher Ron Mahay.[22] He would appear in only two games in the majors[23] before being optioned back to Triple-A on June 4 upon Kyle Farnsworth's return from injury.[24] His appearance on June 1, 2002, would prove to be the final of his Major League career.[12] Following the season, the Cubs declined to offer him a contract and he became a free agent.[25]
Duncan signed with the Chicago White Sox prior to the 2004 season and was assigned to the Triple-A Charlotte Knights to start the season.[28] Duncan spent the bulk of the year in Triple-A but also made four appearances in Double-ABirmingham.[27] He was placed on the disabled list on August 9.[29] It would be his final season in affiliated baseball.[27]
Duncan appeared in a single game for the Jackson Senators of the independentCentral Baseball League in 2005. He faced just two batters, walking one and hitting the other with a pitch. It would his final game in professional baseball.[27] The Senators released him on May 28, 2005.[30]