Benson was the first pick of the 1996 Major League Baseball Draft. After being signed for what was a then-record signing bonus, he spent two years in the minor leagues with the Lynchburg Hillcats and Carolina Mudcats in 1997, and the Nashville Sounds in 1998. Benson made his first major league start on April 9, 1999. He became just the second number one overall pick to win his big league debut. His first strikeout was Sammy Sosa. Benson came in fourth place in the NL Rookie of the Year voting. He came up just shy of breaking the record for most strikeouts in team history by a rookie hurler. His best season came in with Pittsburgh when he posted career-highs in earned run average, strikeouts, innings pitched, and games pitched as well as his only double-digit strikeout games and his career-best three-hit complete game despite the fact that he is a groundball pitcher. That year, Benson broke the record for most strikeouts in Pirates history for a right-handed pitcher. After 2000, he needed Tommy John surgery and missed the entire season. He started the last game at Three Rivers Stadium and the first game ever at Great American Ballpark. Against the Mets, he broke the record for most sacrifice bunts in a game by a pitcher in MLB history with four.