Milt Thompson's journey through Major League Baseball began when he was drafted by the Atlanta Braves in the second round of the 1979 amateur draft. His debut in the major leagues came on September 4, 1984, with the Braves. As an outfielder, Thompson quickly demonstrated his skills on the field, showcasing a solid batting average and speed that made him a valuable asset to his team.

In 1986, Thompson was traded to the Philadelphia Phillies, where he spent several productive seasons. During his time with the Phillies, he became known for his consistent hitting and base-stealing abilities. In 1987, he achieved a career-high batting average of .302, along with 46 stolen bases, which ranked him among the league's top base stealers that year. His performance helped solidify his reputation as a reliable player both offensively and defensively.

Thompson's career took another turn in 1989 when he was traded to the St. Louis Cardinals. With the Cardinals, he continued to be a dependable outfielder, contributing to the team's efforts with his steady batting and fielding. After a brief stint with the Cardinals, he returned to the Phillies in 1993, where he played a crucial role in the team's journey to the World Series. Although the Phillies ultimately fell to the Toronto Blue Jays, Thompson's performance during the season and postseason was commendable.

In 1994, Thompson joined the Houston Astros, where he continued to play as a seasoned outfielder. His tenure with the Astros was followed by a return to the Braves in 1996, where he concluded his playing career. Throughout his time in the major leagues, Thompson was known for his speed on the bases, his ability to hit for average, and his defensive capabilities in the outfield.

After retiring as a player, Thompson transitioned into coaching, bringing his experience and knowledge of the game to various teams. He served as a coach for the Phillies, among other teams, helping to develop and mentor younger players. His post-playing career in coaching further demonstrated his enduring connection to the sport and his desire to contribute to the development of future baseball talent.