Butler first signed with the Blue Jays as an amateur free agent on September 24, 1990, and made his major league debut with them . on June 12, 1993. He played in 17 regular season games and was sidelined by a hand injury he suffered when attempting to steal a base. In his 17-game stint in 1993, he had a .271 batting average with four doubles, two RBIs and 12 strikeouts. He also drew seven walks and went 2-for-4 stealing bases. In the 1993 World Series, won by Toronto, Butler went 1-for-2 with a pinch hit single off Curt Schilling of the Philadelphia Phillies, and became the only Canadian player to have won a World Series with the Blue Jays.

In 1994, Butler played in 41 games for the Blue Jays, batting .176 with one triple and five RBIs. Much of this season was split between the Blue Jays and their Triple-A affiliate, the Syracuse Chiefs. On December 5, 1994 he was traded to the Phillies.

With the Phillies organization, Butler spent much of it in their minor league system, but was called up in 1997, and he played in 43 games, batting .292 with nine doubles, one triple, and 13 RBIs.

On December 22, 1997, Butler signed with the Houston Astros and spent 1998 in their minor league system.

On December 23, 1998, he returned to the Blue Jays as a free agent and appeared in eight games with the Jays during the 1999 season, playing his last game as a Major League Baseball player on July 10, 1999.

In 2001, Butler joined the semi-pro Toronto Maple Leafs of the Intercounty Baseball League as an outfielder. He was also joined by his brother Rich Butler, and later by former Blue Jays pitcher Paul Spoljaric. For much of those years, Rob finished the season as the team’s batting leader, and in 2002, he won the league championship with them. In 2005, Butler played his last game with the Leafs, announcing his retirement from the game.