In his 13-year major league career, Johnson batted .261 with 136 home runs, 609 RBI, 564 runs, 1252 hits, 242 doubles, 18 triples, and 33 stolen bases in 1435 games.

Johnson began his managerial career in 1979. He won pennants in each of his three seasons in the minors and advanced quickly through the New York Mets farm system. He took over the parent club, which hadn't won a pennant since 1973 and was eager for success. Johnson went on to become the first National League manager to win at least 90 games in each of his first five seasons, winning the World Series in 1986 against the Boston Red Sox. Ironically, while with the Baltimore Orioles, Johnson made the final out to clinch the Mets' first ever World Championship in 1969.

He was let go by the Mets when the team struggled during the 1990 season, and was hired in 1993 by the Cincinnati Reds to revive their club. He enjoyed almost immediate success there in guiding the team to the Central Division lead at the time of the 1994 players' strike, and following up with the Division title in 1995. But friction with team management led to his departure after that season, and he returned to Baltimore to become the Orioles' manager. Again, he breathed new life into a struggling franchise as the Orioles earned a wild-card playoff berth in 1996 and the American League's Eastern Division title in 1997. However, disagreements with ownership over issues such as having Roberto Alomar make out a check for a fine to a charity run by Johnson's wife without front-office authorization led to his resignation the day after he was named American League Manager of the Year. His knack for turning teams around would fail, however, in a two-year term as manager of the Los Angeles Dodgers, who had beaten Johnson's heavily favored Mets in seven games in the 1988 National League Championship Series, in 1999-2000.

Johnson managed the United States team to a seventh-place finish out of an 18-team field in the 2005 Baseball World Cup, held in The Netherlands. The team finished tied for second in its group during group play with a 6-2 record before falling, 11-3, to eventual winner and 24-time World Cup champion Cuba in the quarterfinals. A subsequent 9-0 loss to Nicaragua put the Americans into the seventh-place game with Puerto Rico, where they prevailed with an 11-3 win.

Johnson also served as bench coach for Team USA during the 2006 World Baseball Classic.

On June 7, 2006, Johnson was hired by the Washington Nationals as a consultant to team general manager Jim Bowden. Bowden was the general manager of the Cincinnati Reds when Johnson served as the team's manager.