As a child, Baerga dreamed of becoming a member of the Santurce Crabbers. This dream would not come true, however, until well after he had begun his career in the major leagues.

In 1985, at the age of sixteen, Baerga was signed by the San Diego Padres, who later traded him to the Cleveland Indians. Baerga debuted as a major league baseball player with the Indians, on April 14, 1990. That year, he 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 for an average of .288 in 1991, getting 20 home runs and averaging .312 in 1992, and with 21 home runs and an average of .321 in 1993. In 1992, he reached two hundred hits in one season for the first time, hitting 205 hits that year. In 1993, he again reached the mark of 200 hits, with exactly 200. The switch-hitting Baerga was the first of two 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 against the New York Yankees pitchers Steve Howe and Steve Farr in the games 7th Inning. On August 29, 2002 he was joined by Chicago Cubs utility player Mark Bellhorn, who completed the feat against the Milwaukee Brewers.

During the 1994 season, his average numbers fell, due to the strike-shortened season. He hit 19 home runs and maintain an average of .314 at the plate.

1995 was another year plauged by the on-going strike. When baseball resumed, Baerga quickly got back into the swing of things, getting 175 hits and 15 home runs in 139 games. He hit for .314. 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 1996, before being traded to the New York Mets. He collected 129 hits with twelve home runs that year, hittin only for .193 after being traded to the Mets. He ended that year hitting for an average of .254.

Over the next two season with the Mets, Baerga had below average seasons, hitting nine home runs and batting .281 in 1997, and seven home runs and .266 in 1998.

1999 was a year marred by injuries for Baerga, who saw little action playing for the San Diego Padres. Part way into the season, he returned to the Indians for a short period of time. However after playing only 55 games Baerga felt that with his injuries he could no longer perform as a MLB player.

He retired, and bought the Crabbers, becoming player-manager and realizing his childhood dream. However, after only one season, the Crabbers were forced to move to Bayamon, where they became the Cowboys.

In 2002, Baerga returned to Major League Baseball. That year, he got 52 hits as a Boston Red Sox, primarily serving as a pinch-hitter and designated hitter.

In 2003, he was traded to the Arizona Diamondbacks, where he collected 71 hits for the team. The Diamondbacks re-signed him for 2004, but the aging Baerga, now prone to injury, got hurt again and was only able to play 20 games for the Diamondbacks that season. He was signed by the Washington Nationals to a minor-league contract before the 2005 season.

Carlos Baerga has collected 1,543 hits in his MLB career, with 132 home runs, and a batting average of .292.

Although the majority of his playing days are over, Carlos Baerga was one of the players to agree to play for Puerto Rico in the 2006 World Baseball Classic, representing the island Nation. While he will likely be primarily a pinch hitter, the team features fellow Puerto Ricans Ivan Rodriguez, Sandy Alomar, Jr. as catchers, Carlos Beltran, Bernie Williams, Jose Cruz, Jr. and Luis Matos as outfielders, Carlos Delgado, Mike Lowell, José Vidro, Felipe Lopez, and Alex Cintron as infielders, and pitchers Javier Vazquez, Joel Pineiro, J.C. Romero, Jorge Sosa and Kiko Calero amongst others, in a team managed by Saint Louis Cardinals third base coach Jose Oquendo.