He played for the Boston Red Sox, Detroit Tigers, San Diego Padres, Tampa Bay Devil Rays, and New York Yankees of Major League Baseball between 1992 and 2005.

Flaherty grew up in West Nyack, New York and graduated in 1985 from Saint Joseph Regional High School in Montvale, New Jersey.

He attended George Washington University, graduating in 1990[1] with a BA in Speech Communications and a minor in Psychology.

In 1996, the Tigers traded Flaherty to the San Diego Padres, along with Chris Gomez, for Brad Ausmus, Andújar Cedeño, and a minor leaguer.

In 1997, the Padres traded Flaherty to the Tampa Bay Devil Rays for Andy Sheets and Brian Boehringer.

On May 15, 2009, Flaherty was awarded an honorary Doctorate of Humane Letters from St. Thomas Aquinas College in Sparkill, New York.