Pavano was selected in the 13th round of the 1994 draft by the Boston Red Sox. He started his Major League career with the Montreal Expos in 1998, with whom he spent his first four-and-a-half seasons.
Pavano was traded to the Marlins in the middle of the 2002 season along with Graeme Lloyd, Mike Mordecai, Justin Wayne and Donald Levinski for Cliff Floyd, Wilton Guerrero, Claudio Vargas and cash. As a spot starter and long reliever, he posted a 3-2 record in 22 games with a 3.79 ERA.
Over the next two seasons, Pavano was a regular part of the Marlins rotation, making 63 starts (out of 64 total appearances).
2003 saw Pavano post a 12-13 record with a 4.80 ERA. He also went 2-0 over eight games in the playoffs, keeping his ERA below 1.50 and helping the Marlins to their second World Series title.
In 2004, Pavano posted an 18-8 record, his win total good for second best in the NL. His ERA of 3.00 and his 1.174 WHIP were also amongst the NL top 10. He was selected to his first (and thus far only) All-Star appearance for his performance.
In total, Pavano collected 33 wins against 23 losses with a 3.64 ERA.