Penny was selected by the Arizona Diamondbacks in the fifth round of the 1996 draft. In 1999, the Diamondbacks sent Penny, along with Abraham Nunez and Vladimir Nunez to the Marlins for Matt Mantei.
Penny made his Major League debut with the Marlins in 2000, posting an 8-7 record and a 4.81 ERA. In 2001, Penny went 10-10 with a 3.69 ERA in 31 games for Florida. His 1.156 WHIP was good for sixth best in the National League.
In the Marlins push to the World Series Championship in 2003, Penny went 14-10 in the regular season, also flashing power at the plate with two home runs. He added three more wins in the playoffs, including two against the AL Champion New York Yankees.
Penny held down his slot in the order for five seasons in Florida, accumulating 48 wins and 42 losses, along with a 4.07 ERA. He struck out more than twice as many batters as he walked, demonstrating control and occasional power.
The Marlins traded Penny, along with Bill Murphy and Hee Seop Choi, to the Los Angeles Dodgers for Paul Lo Duca, Juan Encarnacion and Guillermo Mota. He has since played for the Boston Red Sox, the San Francisco Giants, the St. Louis Cardinals and is currently on the Detroit Tigers active roster.