He played in Major League Baseball (MLB) for the Texas Rangers, Oakland Athletics, Detroit Tigers, Boston Red Sox, Tampa Bay Devil Rays/Rays, Chicago Cubs, Houston Astros, and Kansas City Royals.

Although Peña was born in Santo Domingo and his family is from San Francisco de Macorís, he spent a significant portion of his childhood in the United States.

As a collegiate player, he competed in the Cape Cod Baseball League (CCBL), which showcases top amateur prospects every summer.

He made his big league debut on September 5, starting at first base, wearing number 15, and going hitless in three at-bats.

[6] On January 14, 2002, along with Mike Venafro, Peña was traded by the Rangers to the Oakland Athletics for Jason Hart, Gerald Laird, Ryan Ludwick, and Mario Ramos.

Peña made his Tigers' debut the next day against the Boston Red Sox, as he went 3–4 with 2 doubles and 2 RBIs.

[6] On May 27, 2004, against the Kansas City Royals, Peña matched a Tigers' nine-inning, single-game record with a career-high six hits.

While with the Tigers, Peña hit the longest home run, a 461-foot blast, in Comerica Park history.

On August 17, 2006, Peña signed a minor league contract with the Red Sox and was assigned to Triple-A Pawtucket.

He was a defensive replacement and when he batted in the bottom of the ninth, he hit a walk-off home run off Brandon McCarthy of the Chicago White Sox.

Peña signed a minor league contract with the Tampa Bay Devil Rays on February 1, 2007 with an invitation to spring training.

With a knee injury to Greg Norton on the last day of spring training, the Rays re-signed him, this time to a Major League contract on April 1.

Peña had a slow start to his 2007 season, batting .213 with four home runs in the month of April as a backup player.

Peña hit .356 with six home runs and 15 RBIs in May as an everyday player and was the Rays' first baseman for the rest of the season.

Peña's season led to his being named the 2007 American League Comeback Player of the Year and he was considered as an AL MVP candidate.

He returned to action from the disabled list on June 27, and finished the season with a .247 batting average, 31 home runs, and 102 RBIs.

[10] One of his home runs, on September 19 against the Minnesota Twins, was the result of the first call overturned by instant replay in MLB history.

[11] After the 2008 season ended, he was awarded his first (and also the first for a Tampa Bay Rays franchise player) AL Gold Glove.

Peña was elected for the 2009 Major League Baseball All-Star Game, replacing Dustin Pedroia and participated in the 2009 Home Run Derby where he lost in a bat-off against Albert Pujols in the first round.

On September 7, 2009, Peña suffered two broken fingers after getting hit by a pitch, which put him out for the rest of the 2009 season.

[12] Despite missing the last few weeks of the season, he still finished tied for the lead for home runs in the American League at 39 with Mark Teixeira of the New York Yankees.

[13] Peña's three-year contract with the Rays, reported by the St. Petersburg Times as worth $24.125 million, expired at the end of the 2010 season.

[32] Peña first became eligible for the National Baseball Hall of Fame during the 2020 balloting, but he received no votes and was removed from future consideration.

[33] In September 2017, Peña appeared on New England Sports Network (NESN) as a studio analyst, and also worked as a color commentator with Jerry Remy and play-by-play announcer Dave O'Brien during the Red Sox' final series of the regular season, against the Houston Astros.

In February 2019, Peña was announced as part of the NESN broadcast team for the Red Sox' 2019 season, to fill in when regular color commentators Jerry Remy and Dennis Eckersley are not available.

In January 2024, Peña was announced as part of the Detroit Tigers Bally Sports Detroit broadcast team for the Tigers' 2024 season, to handle color commentary for multiple games alongside play-by-play announcers Jason Benetti and Dan Dickerson.