Farnsworth graduated from Milton High School in Alpharetta, Georgia, in 1994. During high school, he played baseball, basketball, and football. He continued to play baseball in college at Abraham Baldwin Agricultural College (ABAC) in Tifton, Georgia. Farnsworth is a member of the Church of Jesus Christ of Latter-day Saints. Kyle was inducted into the ABAC Athletics Hall of Fame in 2011.
Farnsworth was drafted in the 47th round by the Chicago Cubs in 1994. He played for the Cubs from 1999 to 2004. He was the winning pitcher in the final baseball game played at Three Rivers Stadium on October 1, 2000. Farnsworth was involved in a brawl in the 2003 season, against the Cincinnati Reds. Reds pitcher Paul Wilson stepped out of the batter's box after an inside pitch, and started to yell at Farnsworth. Farnsworth then met Wilson a short distance from home plate, and speared him to the ground. He was suspended three games for his actions, but MLB reduced the suspension to two games.
In the 2004 season, Farnsworth angrily kicked an electric fan in the Cubs' dugout after an outing in which he gave up six runs in one inning to the Houston Astros. Farnsworth ended up severely bruising and spraining his knee in the process, and was placed on the disabled list as a result.
On February 9, 2005, he was traded to the Detroit Tigers for Roberto Novoa, Scott Moore and Bo Flowers. Farnsworth was involved in a bench-clearing fight in the 2005 season while playing for the Detroit Tigers, against the Kansas City Royals at Comerica Park. After order appeared to have been restored, Farnsworth tackled Royals pitcher Jeremy Affeldt. Farnsworth was ejected from the game.
On July 31, 2005, he was traded to the Atlanta Braves for pitchers Zach Miner and Román Colón.
Following the season, Farnsworth signed with the New York Yankees, replacing Tom Gordon as the team's primary set-up man. The deal, worth $17 million over three years, was the second-highest offer Farnsworth received. The Texas Rangers reportedly offered a three-year, $16.5 million contract with a vesting option that would have taken the deal to $21 million, plus incentives.
He struggled in the 2006 season, accumulating a 4.36 ERA. His struggles continued into the 2007 season.
On July 30, 2008, Farnsworth returned to the Tigers in a trade for Iván Rodríguez.
On December 13, 2008, the Royals reached an agreement with Farnsworth on a two-year, $9.25MM deal. On June 17, 2009, Farnsworth's left, non-pitching hand was bitten while he was breaking up a fight between two of his American bulldogs—Strike and Rambo. The cuts were deep enough to reach, but not cut, a tendon. Farnsworth later taped his finger, tucked it into his glove, and went to practice telling manager Trey Hillman that he could pitch. When asked which of his dogs bit him, Farnsworth replied: "I don't know. I reached in there and started grabbing dogs and throwing dogs. And one of them got me. One of those things that happens. It's never pretty. I've had to do it a few times, and it's ugly."
On July 31, 2010, Farnsworth was re-acquired by the Braves along with Rick Ankiel for Gregor Blanco, Jesse Chavez and Tim Collins.
On January 15, 2011, Farnsworth agreed to a one-year, $3.25 million deal with the Tampa Bay Rays. On February 5, 2013, Farnsworth signed a one-year contract worth $1.25 million. He was designated for assignment on August 9, 2013 and released the next day.
Farnsworth signed with the Pittsburgh Pirates on August 16, 2013 and recorded his first Pirates save against the Texas Rangers on September 11, 2013.
Farnsworth signed a minor league deal with the New York Mets on February 3, 2014. He was released on March 23. On March 26 the Mets re-signed Farnsworth to a minor league contract. He was called up to the majors on April 2 to replace the injured Bobby Parnell.
On April 20, Farnsworth was named the new Mets closer after another blown save by Parnell's replacement, José Valverde. Farnsworth earned his first save as closer the next day in a 2-0 shut out of the St. Louis Cardinals. Farnsworth earned his second save as Mets closer 3 days later on April 23, giving up a run on 3 hits but managing to hang on for a 3-2 win over the Cardinals. The next day on April 24, Farnsworth was passed up for a save opportunity in favor of Daisuke Matsuzaka. However, after the game, Mets manager Terry Collins stated that Farnsworth was still the closer and that the Matsuzaka was the back up option. On April 26, Farnsworth gave up a 10th inning home run to Miami Marlins catcher Jarrod Saltalamacchia, allowing Miami to go on to win 7-6, and earning Farnsworth the loss. On May 3 in a game against the Colorado Rockies, Farnsworth gave up a walk off two run homerun to pinch hitter Charlie Culberson, earning Farnsworth a blown save and his second loss of the season. On May 10, Farnsworth earned his third loss of the season, giving up a go ahead single to Ryan Howard, which resulted to a 5-4 loss to the Philadelphia Phillies. Farnsworth rebounded on May 12, getting his third save of the season in the opening game of the Subway Series against cross town rivals the New York Yankees. This was Farnsworth's last appearance as a member of the Mets.
On May 14, the Mets outrighted Farnsworth to Triple-A to avoid guaranteeing him a full season's contract. Farnsworth stated that he would refuse the assignment and wanted to find a new team that would allow him to "play against this team". The next day on May 15, Farnsworth officially elected free agency.
On May 17, 2014, Farnsworth signed a major league deal with the Houston Astros. He was outrighted off the roster on June 26 and elected to become a free agent.
Midway through the 2015 Mexican Baseball League season, Farnsworth signed with Pericos de Puebla. The next year, he signed with Algodoneros de San Luis, before later joining the Broncos de Reynosa.