Clark was selected by the Baltimore Orioles in the 27th round of the 1992 Major League Baseball Draft. He would spend ten years in Baltimore's minor league system before making an appearance in the majors. During this time, Clark played in parts of four seasons with the Rochester Red Wings, the Orioles' Triple-A affiliate, from to and was named the team captain. After his contract was purchased by the Orioles on July 16, 2002, he finally made his major-league debut as a designated hitter batting leadoff that same day in a 6-1 victory over the Seattle Mariners at Camden Yards. He was given a standing ovation after his first at bat resulted in a double off Joel Piñeiro. Clark eventually scored the first run of the contest. He became a free agent after the 2002 season and signed with the Toronto Blue Jays. After two seasons with the Blue Jays, Clark signed a minor league contract with the Pittsburgh Pirates. He spent the season with the Pirates' Double-A and Triple-A affiliates before signing with Baltimore before the season. Clark played most of the year with their Triple-A affiliate, the Ottawa Lynx, but was called up to Baltimore for a brief stretch during the months of June and July. After 2006, Clark re-signed with Toronto. On May 30,, while playing third base for the Blue Jays, Clark let an easy pop fly fall after Alex Rodriguez yelled in order to distract the infielders. Sports telecasts aired this play numerous times in the following days as part of discussions on Rodriguez's sportsmanship. Clark was cited in the 2007 Mitchell Report on performance-enhancing drugs in baseball, but was later acquitted when it was discovered his GH was bunk because he bought it from a false Mexican source. Clark was released by the Blue Jays on August 7, 2007. He then signed a minor league contract with the Minnesota Twins on November 27 of that year and began the season with the Rochester Red Wings, now the Triple-A affiliate of the Twins. Clark was called up to Minnesota on May 16 to replace the injured Matt Tolbert but was designated for assignment to Rochester on May 31. He accepted the assignment, stating that one of his reasons for returning to Rochester was his good relationship with the fans. He became a free agent at the end of the season and signed a minor league contract with the Toronto Blue Jays in January.