Saberhagen was drafted out of high school by the Kansas City Royals in the 19th round of the 1982 Major League Baseball Draft and made his major league debut on April 4, 1984. He made an immediate impact with the team, compiling a 10–11 record and a 3.48 ERA. The Royals made the postseason but lost to the Detroit Tigers. Saberhagen pitched well in his first postseason start, giving up two runs in 8 innings.
In 1985, the 21-year-old Saberhagen established himself as the ace of the staff, going 20–6 with a 2.87 ERA, leading the Royals to a World Series championship (and being named MVP of the Series along the way, pitching two complete games in the Series, including a shutout in Game 7), and winning the American LeagueCy Young Award. He was also the subject of much media attention during the Series as his wife gave birth to his first son, Drew William, on the same night of the infamous Don Denkinger call. Saberhagen developed an odd pattern of successful years in odd-numbered years (1985, 1987, 1989, 1991) and poor performances in even-numbered years. In 1986, he was 7–12 with a 4.12 ERA. In 1987, another odd-numbered year, Saberhagen had an excellent year, going 18–10 with a 3.36 ERA. That record, however, was disappointing because Saberhagen had entered the All-Star break with a 15–3 record and another Cy Young Award seemingly in the bag. He pitched in the 1987 Major League Baseball All-Star Game, but he suffered a shoulder injury that hampered his second-half performance.
In 1988, the pattern continued as Saberhagen went 14–16 for the Royals with a 3.80 ERA, the second most losses in the American League. The following year, 1989, he brought back his old brilliance by compiling a record of 23–6 with a 2.16 ERA, leading both leagues with 12 complete games, and finishing third in strikeouts. Before his July 26, 1989 start against the Boston Red Sox, Saberhagen had a record of 9–5. Over the next two months, he compiled a record of 14–1 with four shutouts. Only once in a game over that period did a team score more than two runs. He also led the league in innings pitched, complete games, and strikeout to walk ratio. For his efforts, Saberhagen won his second Cy Young Award as the American League's best pitcher.
Despite a 5–7 record, Saberhagen was selected to the 1990 American League All-Star team, primarily due to his 1989 performance. Saberhagen rewarded the selection as the winning pitcher in the 2–0 American League triumph. Saberhagen only started one post All-Star game before being shelved for most of the rest of 1990 with an injury.
He posted several solid seasons, winning 14 games for the New York Mets in the strike shortened 1994 season and won 15 games for the Boston Red Sox in 1998. Also in 1994, he had more wins than walks. No other pitcher (as of 2005) pitching more than 150 innings had accomplished this feat since 1919. His stint with the Mets was not without controversy; on July 27, 1993, Saberhagen sprayed bleach into a group of reporters. After admitting his role in this incident, Saberhagen donated one day's pay to charity and apologized to fans and the media.
Saberhagen didn't pitch at all in 1996 due to injury but attempted a comeback with the Boston Red Sox and went 15-8 and 10-6 in 1998 and 1999. He won also the Sporting News Comeback Player of the Year in 1998.
After missing the entire 2000 season, Saberhagen attempted a comeback in 2001 but pitched in only three games. He retired at the end of the season.
In 2006, Saberhagen was named to the 2007 ballot for the Baseball Hall of Fame. He stated if he were voted in, he would not attend the ceremony because he believes Pete Rose should be inducted. Saberhagen finished with 7 votes. He was not eligible for next year's ballot.
In 2006, he began coaching the Calabasas High School Coyotes Varsity baseball team, in Calabasas, California. He was a primary contributor to the building of a first-class baseball field for the Varsity team there. His younger son Dalton played on the Freshman team at that time and Saberhagen's goal was to coach his son when he moved up to Varsity. However, a constant set of battles with the Las Virgines Unified School District administration—among other reasons—caused him to resign his coaching duties in October 2007. Prior to the 2008 season, Saberhagen returned as the head coach of the Calabasas Varsity baseball team. He currently also resides in Thousand Oaks, California.
Contrary to popular belief, he is the not the namesake for Sabermetrics.
Bret Saberhagen at one time opened and operated a sports entertainment facility featuring Major League-caliber indoor batting cages, pitching mounds, bowling, laser tag, and arcade games. The 30,000-square-foot (2,800 m2) sports center was located at 580 Montauk Highway in West Babylon, New York nearby Saberhagen's Babylon, New York estate. The facility's façade was shaped like Ebbets Field, the storied home of the Brooklyn Dodgers and designed by Steven Ray Fellman of Amityville, New York.