Franklin was drafted by the Seattle Mariners in the 23rd round of the 1992 MLB draft but chose to return to school. He signed his first MLB contract with the team on May 21, 1993. He made his MLB debut in 1999, appearing in 6 games. In 2000, he began the season in Triple-A, and then decided to not play at the MLB in September in order to participate in the Olympics. During those Olympics in Sydney, he and his teammates won a gold medal, defeating Cuba 4-0 in the title game. After missing the 2000 season in the big leagues, Franklin posted a strong spring training and won a job in the Mariners bullpen, appearing in 38 games. The next season, Franklin began the season in the bullpen but after the first half of the season, was moved to the rotation. He finished with a record of 7-5 in 41 appearances, 12 starts. In 2003, Franklin began in the rotation and was one of the Mariners most consistent starters, posting an ERA of 3.57 in 212 innings. He tied for the Major League lead in home runs allowed in 2003, with 34. In 2004, Franklin and the whole Seattle team struggled, losing 99 games. Franklin for his part went 4-16 with a 4.90 ERA in 200 innings. He struck out a career high 104. In 2005, he went 8-15 with a career high 5.10 in 190 innings. He struck out 93. After the 2005 season, Franklin filed for free agency.
Philadelphia Phillies
On January 13, Franklin signed a one-year, $2.5 million contract with the Philadelphia Phillies. Franklin shifted back to a bullpen role, appearing in 46 games.
Cincinnati Reds
On August 7, 2006, Franklin was traded to the Cincinnati Reds for a player to be named later, who turned out to be minor league pitcher Zac Stott. Franklin pitched the rest of the season out of the bullpen, appearing in 20 games.
St. Louis Cardinals
On January 22,, Franklin signed with the St. Louis Cardinals on a one-year, $1 million contract. He signed a two-year, $5 million contract extension with a $2.75 million club option for 2010 on July 5, 2007. He was promoted to closer on May 17,. Franklin was named to the 2009 All-Star Game roster. On September 1,, Franklin signed a two-year, $6.5 million contract extension with the Cardinals. In 2009, he finished the regular season with a 1.92 ERA, and 38 saves. On April 19, 2011, Franklin was removed from his closer role after blowing four saves in five chances to start the 2011 season. Despite the poor season he is still considered a World Series Champion in 2011 with the St. Louis Cardinals. He was released on June 29, after recording an 8.46 ERA, giving up 44 hits, nine home runs, walking seven and striking out 17 in 27 2/3 innings for a 1.84 WHIP in 21 games with the Cardinals in 2011. He retired on December 9, 2011.
He is married to Angie Romberg and the couple has four children: Logan, Teegan, Casen, and Kaylin. He and his family live in Shawnee, Oklahoma. His nephew, Kohl, is also a baseball player. On August 2,, Franklin became the eighth MLB player, and second Mariner, to test positive for steroid use, receiving a ten-day suspension. On December 13,, he was named in the Mitchell Report to the Commissioner of Baseball of an Independent Investigation Into the Illegal Use of Steroids and Other Performance Enhancing Substances by Players in Major League Baseball.
