[2] 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.

[1] Báez eventually learned the language through trial and error in a process that lasted for three years, memorizing words before knowing their actual meaning.

[9] Promoted to the Boise Hawks of the Class A-Short Season Northwest League, Báez recorded one single in six at bats across two games.

[12] 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.

[14] 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.

[21] 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.

[22] 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.

[30] Bothered by a back injury, he opened his participation with the Iowa Cubs of the Class AAA International League (IL) immersed in a slump, with his only hit in 20 at bats being the first home run of the season.

[31][32] 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.

[34] 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.

[39] 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.

After struggling in spring training, mostly due to a high number of strikeouts, the Cubs optioned Báez to Iowa on March 30, 2015.

In Game 4, Báez drove in Jason Heyward to cap off a four-run rally in the top of the ninth, sending the Cubs to the 2016 National League Championship Series with a 6–5 victory.

[47] During the first game of the 2016 National League Championship Series against the Los Angeles Dodgers, Báez stole home in the second inning.

[54] On May 27, in an 8–3 victory against the San Francisco Giants, Báez hit his 13th home run of the year and became the first Cubs player with at least 40 RBIs before Memorial Day since Derrek Lee in 2005.

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.

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.

[63] Báez attributed his struggles at the plate with the ban of in-game video review that MLB implemented in the aftermath of the Houston Astros' sign-stealing scandal.

The throw pulled the first baseman off the bag toward home plate, which allowed the Cubs player on second (Willson Contreras) to safely reach third, who briefly paused in anticipation for the tag out.

[68] On July 30, 2021, Báez was traded to the New York Mets along with Trevor Williams and cash considerations in exchange for Pete Crow-Armstrong.

[69] He decided to wear number 23, along with former teammate Kris Bryant, to honor Cubs' Hall of Famer, Ryne Sandberg.

[70] On August 24, Javier Baez moved to second base after his childhood friend Francisco Lindor was activated off the injured list and took over his primary position at shortstop.

In the game following his controversial remarks, Baez scored a game-winning run to complete a Mets ninth-inning comeback against the Miami Marlins.

In his Tigers debut on April 8, 2022, Báez hit a ninth-inning walk-off single to defeat the Chicago White Sox, 5–4.

[83] In the two games after being benched, the Tigers went 2–0 and Báez went 4-for-8 on ten at-bats, two doubles, four runs batted in, two walks, two strikeouts, and an OPS of 1.350.

On June 21, Báez collected his 1,000th career hit, an RBI single off Brady Singer of the Kansas City Royals.

[85] Báez struggled through July of the 2024 season, having what Chris Kirschner of The Athletic called "the worst contract in baseball and possibly .

[94] Baéz finished the tournament as the stolen bases leader and being voted as the second baseman of the 2017 All-World Baseball Classic team.

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.

[123] Báez's wife, Irmarie, is the sister of Jannieliz Márquez, who is married to Puerto Rican pitcher José Berríos.