In 1985, Alomar signed with the San Diego Padres at age 17, and joined the team’s Class-A affiliate, the Charleston Rainbows. The following year, playing for the Reno Padres, he won the California League batting title with a .346 average.

Alomar made his major league debut on April 22, 1988 against the Houston Astros, recording a hit in his first at bat, off of Nolan Ryan. With the Padres, he established himself as a solid hitter and baserunner, and defensively, he displayed excellent lateral range and a powerful arm, often making spectacular plays on ground balls hit deep in the hole between first and second base, and on balls hit up the middle, well behind second base. He became an All-Star for the first time in 1990, as a reserve player for the National League.

On December 5, 1990, Alomar and Joe Carter were traded to the Toronto Blue Jays in exchange for Fred McGriff and Tony Fernández. It was in Toronto that he developed into a premier offensive second baseman, combining a .300-plus batting average with power and high end speed on the bases. In 1991, he capitalized on his speed with 11 triples and 53 stolen bases, leading the team to its first of three consecutive playoff appearances. The following year, he scored 105 runs, drew 87 walks, and had a .405 on-base percentage. In 1993, Alomar had his best season with the Blue Jays, producing 17 home runs (HR), 93 runs batted in (RBI), and 55 stolen bases, while batting .326, third in the American League behind teammates John Olerud and Paul Molitor. He was a central figure in Toronto’s World Series championships in 1992 and 1993; in Game 6 of the 1992 World Series, he scored the series-winning run on Dave Winfield’s two-run double in the 11th inning. Alomar’s game-tying, ninth-inning home run against Oakland relief ace Dennis Eckersley, in Game 4 of the 1992 American League Championship Series (ALCS), is considered by many as the most important hit in the club’s history, as the team’s three previous trips to the ALCS had ended in disappointment; he was named the Most Valuable Player (MVP) of the series. In 1995, he played 104 consecutive games without committing an error, setting an AL record for second basemen. In each of his five seasons with the Blue Jays, Alomar was named to the All-Star team and won the Gold Glove Award.

Time called Alomar “the best second baseman of t[his] generation” and he is regarded as one of the greatest second basemen and all-around players of all time. Known for his acrobatic and flamboyant style of defense, Alomar won 10 Gold Glove Awards, establishing a major league record for second basemen. He ranks in the top 10 of several all-time categories for second basemen, including games played, stolen bases, plate appearances, doubles, assists, hits, runs, at bats, and double plays turned. In a 17-year career, he was a .300/.371/.443 hitter with 210 home runs and 1,134 RBI; his .307 career batting average as a member of the Blue Jays is a franchise record. He was the Blue Jays Player of the Year in 1991, 1992, and 1995, as well as the Cleveland Indians Man of the Year in 1999 and 2001. A clutch hitter, Alomar had a .313 postseason average, including a .347 average in two World Series appearances. His game-tying home run in Game 4 of the 1992 ALCS is often considered the most important hit in Blue Jays history, as it changed the fortunes of the franchise.

On December 21, 1995, Alomar signed with the Baltimore Orioles at a time when Toronto was looking to rebuild, while Baltimore was improving into a pennant-contending team. In Baltimore, he paired with Hall of Famer Cal Ripken Jr. to form a formidable double-play combination. Alomar appeared in the playoffs in 1996 and 1997 for the Orioles, hitting a series-winning home run in Game 4 of the 1996 American League Division Series (ALDS), although the Orioles were defeated in the ALCS both years. In 1998, he was named the Major League Baseball (MLB) All-Star Game MVP.

On September 27, 1996, during a game against the Blue Jays, Alomar got into a heated argument over a called third strike with umpire John Hirschbeck and spat in his face. He defended himself by saying Hirschbeck had uttered a racial slur and that Hirschbeck had been bitter since one son had died of ALD and another had been recently diagnosed as well. Upon hearing this public disclosure of his private life, Hirschbeck had to be physically restrained from confronting Alomar in the players’ locker room.

Alomar was suspended for the first five regular season games in 1997 and donated $50,000 to ALD research. Alomar and Hirschbeck settled their differences publicly and made apologies to each other on April 22, 1997, standing at home plate and shaking hands in front of the crowd before an Orioles game.

On November 24, 1998, Alomar signed a four-year contract with the Cleveland Indians, joining his All-Star brother, Sandy Jr. It was in Cleveland that Alomar had two of his finest seasons. In 1999, he hit .323/.422 on-base percentage/.533 slugging percentage, with 24 HR, 120 RBI, and 37 stolen bases, and in 2001, he batted .336/.415/.541, with 20 HR, 100 RBI, and 30 steals. Cleveland made the playoffs in 1999, losing in the ALDS to the Boston Red Sox; in 2001, they again made the playoffs, but lost to the Seattle Mariners in the ALDS. Alomar finished third in AL MVP voting in 1999 and fourth in 2001.

On the field, Alomar teamed with shortstop Omar Vizquel to form another decorated middle infield combination. In 2000, with Vizquel committing just three errors all season long, the entire Cleveland infield committed 34 errors—just one more than the record low set by the New York Mets infield the year before. Vizquel, Alomar and third baseman Travis Fryman each won the Gold Glove Award that season; the Vizquel-Alomar duo ultimately won three consecutive Gold Gloves together, becoming one of just eight shortstop-second baseman duos to have accomplished this feat in the same year.

In 2002, Alomar hit only .266/.331/.376 with 53 RBI and 73 runs scored, while falling apart defensively at second base. The Mets were puzzled by Alomar’s mediocre play, which some attributed to his lack of comfort with being under the greater scrutiny of the New York fans and media. However, not even a midseason trade back to the American League to the Chicago White Sox in 2003 could revive Alomar from his funk. There was more misery ahead with the Arizona Diamondbacks in 2004, including a two-month disabled stint with a broken right hand. On August 5, Alomar returned to the White Sox, and hit just .263/.321/.392 in 56 games.

Alomar agreed to a one-year contract with the Tampa Bay Devil Rays for the 2005 season. However, on March 19, 2005, after a spring training plagued by back and vision trouble, he announced his retirement.

On April 4, 2008, Alomar was inducted into the Blue Jays Level of Excellence at Rogers Centre, prior to the team’s home opener.

Alomar married Puerto Rican model Maripily Rivera on June 1, 2009. The next year, Rivera alleged that she had been victim of aggression from Alomar and that she wanted to end the marriage. Alomar alleged that Rivera had threatened to divorce him unless he gave her half ownership of his Tampa residence. The divorce was finalized on July 12, 2011 with a private settlement.

In 2010, Alomar’s first year of Hall of Fame eligibility, he missed induction by eight votes. His 73.7% of the vote was the highest percentage of votes in any player’s first year on the ballot without being elected. Some baseball writers expressed shock that he failed to get in on the first ballot, but many attributed the near-miss to sportswriters holding a grudge over the 1996 spitting incident with John Hirschbeck, including Alomar’s brother Sandy Jr. and Hirschbeck himself. He was elected to the Hall of Fame in his second year of eligibility, with 90% of the vote (523 of 581 ballots cast). On July 24, 2011, Alomar was inducted into the Hall of Fame, becoming the first inductee to be depicted as a Blue Jays player on his plaque.

On June 19, 2010, Alomar was inducted into the Canadian Baseball Hall of Fame in St. Marys, Ontario.

The 2011 Caribbean Series was dedicated to him, which was followed by his induction into the Caribbean Baseball Hall of Fame.

On March 31, 2011, Alomar was named as a special assistant to the Blue Jays organization. The following year, he began hosting the annual Tournament 12 (T12) showcase at Rogers Centre for Canadian baseball prospects; major leaguers Josh Naylor, Mike Soroka, and Abraham Toro are alumni of the tournament.

On July 31, 2011, the Blue Jays retired Alomar’s number 12 at Rogers Centre; he became the first player in franchise history to receive the honor.

On December 12, 2012, Alomar married Toronto native Kim Perks at the Art Gallery of Ontario. Their first daughter was born in 2014. Alomar resides in Toronto.

On August 3, 2013, Alomar was inducted into the Baltimore Orioles Hall of Fame.

On November 12, 2013, Alomar launched a baseball equipment line, Alomar Baseball.

On September 24, 2015, Alomar was inducted into the Ontario Sports Hall of Fame in Toronto.