Saunders initially signed with the Florida Marlins' minor league system in 1992, a year before their expansion season. He was part of the Marlins' opening day roster in 1997, and finished with a 4–6 record in 22 starts, with his first three wins coming against the Atlanta Braves. The Marlins earned a wild card berth in the 1997 playoffs, and after being left off the Division Series roster, Saunders was placed on the LCS roster against the Braves. He started Game 3 of the series, which Liván Hernández won in relief of Saunders.
In the World Series, Saunders started Game 4 against the Cleveland Indians, but took the loss after giving up six earned runs in two innings pitched; nonetheless, he earned a World Series ring as the Marlins defeated Cleveland in seven games.
Saunders was one of many members of that team who left the Marlins following that season, joining the Rays for their inaugural season after being the first pick in the 1997 MLB Expansion Draft. Saunders was 9th in the American League in strikeouts, but also 1st in walks, as he struggled to a 6–15 record. He started the 1999 season 3–3, but on May 26, while pitching against the Texas Rangers, a bone in Saunders' arm was broken while throwing a pitch in a frightening incident. It was reported that, at the time of the incident, "a pin drop could be heard" inside Tropicana Field. He missed the remainder of the season. In 2000, he broke his arm again in a rehab assignment, forcing Saunders to retire at the age of 26.
In 2005, Saunders announced a comeback, signing a minor league contract with the Baltimore Orioles, and making their spring training roster. He pitched one inning against the St. Louis Cardinals before he was reassigned to the minor leagues. He remained listed on the Bowie Baysox roster for the whole 2005 season, but never pitched in a game, although he did appear in 9 games for the Mesa Miners of the Golden Baseball League.