Charles was originally signed by the Boston Braves in 1952. He spent eight seasons in the Braves’ farm system in the still-segregated Deep South, during which he wrote poetry concerning baseball and racism. Due to the presence of longtime All-Star Eddie Mathews at third base, the Braves traded Charles to the Kansas City Athletics prior to the 1962 season with Joe Azcue and Manny Jiménez for Lou Klimchock and Bob Shaw.

In his rookie season of 1962, Charles batted .288 with 17 home runs, 74 runs batted in and 20 stolen bases; the batting average, home runs and stolen bases would all be career highs. He was also named to the Topps All-Star Rookie Roster. Charles would retain his steady play for the Athletics over the next four seasons; in 1963 he batted .267 with 15 home runs and a career-best 79 RBIs, and while his batting average fell to .241 in 1964 he still managed 16 home runs and 63 RBIs. Prior to the 1965 season, Athletics owner Charlie Finley moved the fences back in Municipal Stadium, and though Charles batted .269 that year and .286 in 1966, his combined home run total was 17—the same number he had hit in his rookie season.

On May 10, 1967, the Athletics traded Charles to the New York Mets for Larry Elliot and $50,000. He would be the oldest regular on his new team. In 1968, he led the Mets in home runs with 15. In 1969, he shared third base duties with rookie Wayne Garrett as a member of the Miracle Mets team that unexpectedly won the World Series, after finishing dead last in five of its first seven seasons and 9th in a 10-team National League in the other two. That year, the Mets had trailed the Chicago Cubs by as many as 10 games in the National League East (both leagues had split into two divisions after expanding from 10 teams to 12) on August 13. On September 24, they clinched the division with a 6–0 victory over the St. Louis Cardinals, with Charles homering off Steve Carlton (his final Major League home run) and Donn Clendenon homering twice and Gary Gentry pitching a four-hitter for the victory.

Ed Charles appears in the 2013 movie 42, played by Dusan Brown. The scene depicts Charles’ meeting with Jackie Robinson, when (after Jackie’s train had long since departed) Charles dashed out and put his ear to the train tracks, enthusiastically declaring that he could still hear the train.

Charles died on March 15, 2018 at the age of 84. Having served in the U.S. Army during the Korean War, where he attained the ranking of Private First Class, he was buried at Leavenworth National Cemetery in Leavenworth, Kansas.