On August 5, the Cubs promoted Báez to the major leagues. In his debut that day, he hit his first career home run; the game-winner in the 12th inning victory against the Colorado Rockies, becoming the first player since Miguel Cabrera in 2003 to hit an extra innings home run in his debut. In his third game, Báez hit two home runs, becoming the first player since Joe Cunningham in 1954 to hit three home runs in his first three MLB games. On August 18, 2014, Báez hit his fifth home run in 14 games, joining Jason Kipnis as the only other second baseman to do so in the last 100 years.

Born and raised in Puerto Rico, Báez moved to Florida in 2005 along with his mother and siblings, two brothers and a sister. The move was so that his sister, Noely, could get medical treatment for her spina bifida condition. In Puerto Rico he and his two brothers, Gadiel and Rolando, became familiar with the sport through their father, Ángel Luis Báez who, before his death when Javier was ten, heavily influenced their life and was responsible for their interest in baseball. The brothers would later immortalize this interest by getting tattoos of Major League Baseball’s logo, which symbolized that “baseball has been in [their] lives forever.” As a middle school student, it took time for Báez to adapt because he was unable to fluently speak or understand English. Báez eventually learned the language through trial and error in a process that lasted for three years, memorizing words before knowing their actual meaning.

On April 10, Báez hit two home runs against the Pittsburgh Pirates. The next day against the Pirates, Báez hit two home runs again. On May 19, Amir Garrett of the Cincinnati Reds struck out Báez and yelled in excitement. Báez approached Garrett and a benches-clearing brawl ensued. On May 27, in an 8-3 victory against the San Francisco Giants, Báez hit his 13th HR of the year and became the first Cubs player with at least 40 RBIs before Memorial Day since Derrek Lee in 2005.

The Chicago Cubs, led by Jim Hendry, selected Báez in the first round, with the ninth overall selection, of the 2011 Major League Baseball draft. He began his professional career by playing shortstop for the Arizona Cubs of the Rookie-level Arizona League, where he only played in three games, recording three hits, including two doubles, in 12 at-bats and two stolen bases. Promoted to the Boise Hawks of the Class A-Short Season Northwest League, Báez recorded one single in six at bats across two games. On September 29, 2011, he was selected third overall by the Leones de Ponce in the Liga de Béisbol Profesional Roberto Clemente’s (LBPRC) rookie draft, but did not play due to the Cubs’ limitations.

Before the 2012 season, MLB.com rated Báez as the 62nd best prospect in baseball. He remained with the Cubs in extended spring training with other prospects, participating in 26 games and hitting 6 doubles, 3 triples, and 8 home runs, with 28 RBI, 11 stolen bases, and 23 strikeouts in 94 plate appearances. He made his regular season debut with the Peoria Chiefs of the Class A Midwest League. He was promoted to the Daytona Cubs of the Class A-Advanced Florida State League (FSL). Baseball America included Báez in two of its “Best Tools” lists, naming him the “Most Exciting Player in the Midwest League” and the “Best Defensive Infielder” in the Chicago Cubs system.

Before the 2013 season, MLB.com rated Báez as the 16th best prospect in baseball. The Cubs invited him to join their major league team in spring training, competing in the Cactus League. Báez hit four home runs in five at-bats over the course of two games, including in an unofficial exhibition game against the Japanese national baseball team that was preparing for the 2013 World Baseball Classic. He concluded spring training with a .298 batting average and 10 RBIs. Báez returned to the Daytona Cubs to open the 2013 season. On June 10, 2013, Báez hit four home runs in one game, becoming the second player to do so in the history of the FSL. Báez was named one of the five finalists in the fan vote for the final spot on the World Team’s roster for the 2013 All-Star Futures Game, but he finished second to Carlos Correa.

On July 6, 2013, the Cubs promoted Báez to the Tennessee Smokies of the Class AA Southern League after displaying more plate discipline and walking more often during the previous month. Báez was named to both the FSL and Southern League All-Star teams at the conclusion of the season. The Cubs named him their Minor League Player of the Year, closing the season as the top-ranked prospect in the team’s system and third overall in the Southern League. On October 28, 2013, Báez won the MiLBY Award for Best Minor League Game of the Year, recognizing his four-home run game.

The Cubs invited Báez to spring training in 2014. An injury suffered by Starlin Castro allowed him regular playing time. To increase his versatility, Báez began practicing at second base and third base. He was reassigned to Minor League camp during the final week of spring training. Bothered by a back injury, he opened his participation with the Iowa Cubs of the Class AAA Pacific Coast League (PCL) immersed in a slump, with his only hit in 20 at bats being the first home run of the season. During the second week of the season, Báez had his first multi-hit game and hit a second home run before being placed on the seven-day disabled list with an ankle sprain. Báez slumped following his return, and his batting average fell below .150 in May, while his strikeout-to-walk ratio worsened. With a more patient approach at the plate, Báez began a hitting streak on May 16, 2014. On May 26, 2014, Báez was named the PCL Player of the Week for the previous week.

On May 22, 2014, the Cangrejeros de Santurce of the LBPRC signed Báez by exploiting a legal loophole that allowed players to be considered free agents unless properly signed within three years of being drafted. However, the Leones de Ponce quickly reclaimed his local player rights, claiming that they had approached him with the intent of formalizing a contract but that the “extreme fatigue” clause of the Winter League Agreement had interfered.

On September 2, Castro injured himself in an awkward slide at home plate in which he sprained his left ankle rendering him unable to play for the remainder of the season. Báez finished the season at shortstop. In 52 games with the Cubs in 2014, Báez struck out 95 times while batting .169 with 5 stolen bases, 9 home runs, and 20 RBI.

After struggling in spring training, mostly due to a high number of strikeouts, the Cubs optioned Báez to Iowa on March 30, 2015. He batted .324 in 70 games for Iowa, missing time due to the death of his sister and a broken finger.

Báez’s sister, Noely, died on April 8, 2015, aged 21. She had spina bifida. Báez took a leave of absence from the Iowa Cubs to help cope with the loss. Báez is left-hand dominant and eats and writes with his left hand, and suggests this helps his game. On August 8, 2019, Báez batted left handed in a game for the first time against Kyle Farmer, an infielder pitching during a 12-5 blowout in the 9th inning. Báez chose “El Mago” (Spanish for “The Magician”) as his nickname for the Players Weekend in 2017 and 2018.

Baéz played for the Puerto Rican national team in the 2017 World Baseball Classic where he won a silver medal. Báez averaged .296 with one home run, five runs batted in and four tournament leading stolen bases. Following the conclusion of the tournament, he was named to the 2017 All-World Baseball Classic team.

On July 9, while batting .294 with 17 home runs, 63 RBIs, and 16 stolen bases, Báez was named the starting second baseman for the 2018 MLB All-Star Game, his first All-Star selection. Báez was only the second player in MLB history to have at least 18 home runs, 18 doubles, 18 stolen bases, and 5 triples by the All-Star break, Willie Mays was the first. Báez also participated in the 2018 Home Run Derby. On August 23, Báez hit a 481-foot home run, the third-longest home run in the MLB in 2018. On September 2, Báez hit his 30th home run of the year and scored his 100th RBI and was the first Cubs middle infielder since 1990 to achieve both in the same year.

Baez in 2018 had 606 at bats with 176 hits and a batting average of .290. He hit 34 home runs, drove in a league leading 111 RBIs and stole 21 bases. He swung and missed at 18.2% of the pitches he saw, second behind only Jorge Alfaro (23.8%) in the NL. He finished second to Christian Yelich of the Milwaukee Brewers in the selection of the Most Valuable Player in the National League. In 2018, Baez was one of three players to record at least 30 home runs, 100 RBI, 100 runs and 20 steals; the other two players were Christian Yelich and Jose Ramirez.

Báez announced his engagement to longtime girlfriend Irmarie Márquez via Twitter on April 11, 2018. Their son, Adrián Javier Báez Márquez, was born on June 28, 2018. The couple was married in San Juan, Puerto Rico on January 26, 2019. Báez’ wife, Irmarie, is the sister of Jannieliz Márquez, who is married to Minnesota Twins pitcher José Berríos.

Baez hit his 100th career home run on June 23, 2019, off of Seth Lugo against the New York Mets. In July, he was named to his second All-Star Game. Báez also hit lefty in a blowout win vs the Reds with Catcher Kyle Farmer pitching. On May 19, Baez injured his heel while making a barehanded pickup and throw on a grounder. Following his injury, Baez had a slash line of .259/.287/.490 with a 96 wRC+, 27.1% strikeout rate, and 3.9% walk rate until he was suffered a fractured thumb on September 1, during a headfirst slide into second base. This effectively ended his 2019 season, though he did have a few pinch hitting and pinch running appearances during the last few games of the year in an effort to boost a slumping Cubs team.

In 2020 he batted .203/.238/.360 in 222 at bats, and had the lowest on base percentage of all qualified NL batters.