On March 17 1996, Walker was traded along with minor leaguer Scott Adair to the San Diego Padres for Roberto Petagine and minor leaguer Luis Arroyo. Walker played one game for the Padres before going to the minors. In 1997, Walker signed with the Boston Red Sox but never played for them at the major league level.
In 2000, Walker made his way back to the major league level with the Colorado Rockies after signing with them in 1998. In December 2000, Walker once again signed with the New York Mets and played 3 games for them before returning to the minors. On May 3, 2002, he was claimed off waivers by the Toronto Blue Jays, with whom he played 124 games between 2002 and 2006. He also played for the Yokohama BayStars of Nippon Professional Baseball in 2004, between his two stints with the Blue Jays.
On July 22, 2006, Walker had shoulder surgery. In 2006, the Toronto Blue Jays released him, but on February 12 2007, the Blue Jays signed him to a minor league contract with an invitation to spring training; he was released toward the end of spring training 2007.[3] He signed with the New York Yankees on May 9, 2007.
On November 7, 2011, Walker was named bullpen coach for the Toronto Blue Jays, following a stint as the pitching coach for the Double-A New Hampshire Fisher Cats, which won the Eastern League title earlier that year.[8]
On November 24, 2012, Walker was appointed as the pitching coach for the Blue Jays, replacing Bruce Walton.[9]
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