After spending his first few seasons with the Pirates minor league affiliates, Shouse was called up to make his MLB debut on July 31, 1993. He played only six major league games that year before returning to the minors.

While still in the minors, Shouse was traded on May 16, 1996 to the Baltimore Orioles. Following the season, he was released by the Orioles and signed with the Boston Red Sox. Shouse made it back to the majors in 1998 with the Red Sox, joining them for seven games.

Shouse shuffled between several teams over the next four seasons, playing strictly in the minors however. Shouse signed as a free agent with the Arizona Diamondbacks on November 11, 1998, then with the New York Mets, Baltimore Orioles and Houston Astros all in 2000.

Finally on December 8, 2001, Shouse signed with the Kansas City Royals, where he saw playing time in the majors again, for 23 games during the 2002 season. Following the regular season, Shouse was released and signed with the Texas Rangers on December 3, 2002. He stayed with the Rangers for just over three seasons, playing in the MLB each year.

On May 13, 2006, Shouse was traded to the Milwaukee Brewers. He was on the full roster for the start of the 2008 regular season.