Boyer attended George Walton Comprehensive High School in Marietta, Georgia. The Atlanta Braves selected him in the third round of the 2000 Major League Baseball draft. His first season of pro baseball was with the rookie league team the Gulf Coast Braves, where he went 1–3 with a 2.51 Earned run average (ERA).
In Boyer's first season, playing for the Atlanta Braves as a midseason call-up, he went 4–2 with a 3.11 ERA in 37.2 innings. Boyer went 4–5 with a 4.52 ERA and 57 strikeouts with the Danville Braves in 2001. The next year, he played with the Class A team the Macon Braves and led the bullpen with 73 strikeouts.
In 2003, Boyer stayed with the Macon Braves when they moved to Rome. That year he finished fifth in the league in wins with 12, and led the team in wins. He finished the year with a 12–8 record and a 3.69 ERA. He also recorded a minor-league career-high 115 strikeouts.
In 2004, Boyer played with Class A Myrtle Beach. He led the Carolina League with 154 innings pitched and was selected to the Carolina League All-Star team. He was elected the Carolina League Pitcher of the Week for the week of May 3 by The Sports Network.
On June 12, 2005, Boyer was called up to the major leagues directly from the AA Mississippi Braves, and made his debut that day against the Oakland Athletics. He went 4–1 with a 2.05 ERA in 23 games at Atlanta's home field, Turner Field.
On May 14, 2008, Boyer pitched 1.1 innings to record his first Major League save, against the Philadelphia Phillies.
On April 20, 2009, Boyer was traded to the St. Louis Cardinals for Brian Barton. On June 4, Boyer was designated for assignment.
On June 8, 2009, Boyer was claimed by the Arizona Diamondbacks.
Boyer signed a minor league contract with the New York Mets on January 21, 2011. The deal included an invitation to spring training. On April 10, 2011, Boyer was designated for assignment.
Boyer signed a minor league contract with the Pittsburgh Pirates on April 20, 2011. He was released on June 18.
Boyer signed a minor league contract with the St. Louis Cardinals on July 5, 2011. He was assigned to the Triple-A Memphis Redbirds. He was released on August 13, after allowing 26 runs in 16 innings for Memphis.
Boyer retired from baseball in 2012. He returned to baseball the next year, when he signed a minor league contract with the Kansas City Royals on January 3, 2013. He was released in May.
Boyer subsequently signed with the Hanshin Tigers of Nippon Professional Baseball after his release from Kansas City.
Boyer signed a minor league deal with the San Diego Padres on January 9, 2014. His contract was selected from the Triple-A El Paso Chihuahuas on May 22. He was designated for assignment on May 25, and outrighted back to El Paso on May 27. He was called back up on June 15. He became a free agent after the season.
On January 7, 2015, Boyer signed a minor league contract with the Minnesota Twins. The team announced that Boyer had made the Opening Day roster on March 30.
On February 12, 2016, Boyer signed a minor league contract with the Milwaukee Brewers with an invitation to spring training, and made the Opening Day roster with a contract worth $950,000.
Boyer signed a minor league contract with the Atlanta Braves on January 17, 2017. He was released on March 25.
On April 3, 2017, Boyer signed a minor league deal with the Boston Red Sox. The Red Sox called up Boyer on May 28 2017.
He is married to Ginsey, with whom he has two sons.
In November, 2015, working with the non-profit Exodus Road, he spent ten days undercover with former MLB first baseman, Adam LaRoche, helping to identify and rescue under-age sex slaves in Southeast Asia.