On November 4,, at the age of sixteen, Baerga was signed by the San Diego Padres. As a 17-year-old he debuted for their Class A affiliate Charleston Rainbows. He played with the team for two seasons. On December 6,, San Diego traded him to the Cleveland Indians along with Sandy Alomar, Jr. and Chris James in exchange for established power-hitter Joe Carter. Baerga debuted as a major league baseball player with the Indians, on April 14,. That year, he played mostly as a third baseman and shortstop and would hit 17 doubles and seven home runs, while averaging.260 at the plate. Over the next four years, his home run and batting averages numbers rose steadily, hitting 11 home runs, and batting.288 in while playing mostly as a third baseman and second baseman, hitting 20 home runs and averaging.312 in while becoming a full-time second baseman, and with 21 home runs and an average of.321 in. In 1992, he reached 200 hits in one season for the first time, getting 205 hits that year. In 1993, he duplicated the mark of 200 hits, with exactly 200. Baerga became the first second baseman since Rogers Hornsby in to have back-to-back 200+ hit, 20+ home run, 100+ RBI, and.300+ average seasons when he accomplished the feat in 1992–93. He was a 3-time All Star in the 1992, 1993, and 1994 seasons. The switch-hitting Baerga was the first of three players to have ever hit one home run from both sides of the plate in the same inning. He did so on April 8, 1993, at Cleveland Municipal Stadium against New York Yankees pitchers Steve Howe and Steve Farr in the game's 7th inning. On August 29,, he was joined by Chicago Cubsutility playerMark Bellhorn, who completed the feat against the Milwaukee Brewers, and on July 30, 2012, Kendrys Morales became the third player to accomplish this rare feat against the Texas Rangers. During the strike-shortened season, Baerga hit 19 home runs and maintained an average of.314 at the plate. In the 144-game season, Baerga had 175 hits and 15 home runs in 139 games, with a.314 average. The Indians made it to the World Series, where they fell to the Atlanta Braves in six games. Baerga played 100 games with the Indians in, before being traded to the New York Mets on July 29, 1996, with Álvaro Espinoza, for Jeff Kent and José Vizcaíno. He collected 129 hits with twelve home runs that year, hitting only.193 after being traded to the Mets. He ended that year with an average of.254. Over the next two seasons with the Mets, Baerga had below average seasons, hitting nine home runs and batting.281 in, and seven home runs and.266 in. He was granted free agency on October 26, 1998.
Decline and retirement
Baerga began to develop problems with his knees. On January 27,, Baerga was signed by the St. Louis Cardinals and released before the season began. The Cincinnati Reds signed him, but after he hit.290 in the minors, released him midseason. The San Diego Padres put him in the minors for 21 games where he hit.286, and brought him up for 33 games where he hit.250. Bought by Cleveland in August, he hit.228 in 31 games with them. Signed briefly by the Tampa Bay Devil Rays in, Baerga did not appear in the majors that year. He felt that he could no longer perform as a major leaguer. In 2001, he signed with the but was released during spring training. In, he played for the Long Island Ducks and in the Korea Baseball Organization, Samsung Lions). Then he retired, and bought the Santurce Crabbers, becoming player-manager and realizing his childhood dream. In 2013, Baerga was elected into the Indians Hall of Fame.
Return to major leagues
In 2002, Baerga returned to the majors. That year, he got 52 hits with the Boston Red Sox, primarily serving as a pinch-hitter and designated hitter. In, he was traded to the Arizona Diamondbacks, where he collected 71 hits for the team. The Diamondbacks re-signed him for, but the aging Baerga, now prone to injury, got hurt again and was only able to play in 20 games that season. He was signed by the Washington Nationals to a minor league contract before the season and played 93 games for them. He also played for Puerto Rico in the 2006 World Baseball Classic. Baerga collected 1,543 hits in his MLB career, with 134 home runs, 774 RBI and a.292 batting average. As a broadcaster, Baerga has enjoyed prominence as a color commentator for Monday Night Baseball retransmissions in Spanish on ESPN Dos for the Mexico-Caribbean-Venezuela region. He is an analyst on Beisbol Esta Noche on ESPN Deportes and ESPN Latin America. He is recognized by fans and fellow co-workers as "Carlos Obed".