Schafer was drafted by the Atlanta Braves in the third round of the 2005 Major League Baseball Draft out of Winter Haven High School. In April 2008 he was suspended 50 games by Major League Baseball after being accused of HGH use. He was the first player to be suspended by Major League Baseball’s Department of Investigations.

Schafer was named the Braves’ starting center fielder for the 2009 season on April 3, 2009, despite never having played at a higher level than Double-A. He made his major league debut on April 5, 2009, becoming the 99th player in Major League Baseball history to hit his first career home run in his first major league at bat, off Brett Myers of the Philadelphia Phillies. He finished the game 2 for 3, with the home run, a single, an intentional walk, and a strikeout.

On June 2, 2009, Schafer was optioned to Triple-A Gwinnett Braves after batting only .204 with 63 strikeouts in 167 at-bats. He was called back up to the major league team on May 24, 2011.

On July 31, 2011, Schafer was traded with Juan Abreu, Paul Clemens, and Brett Oberholtzer to the Houston Astros in exchange for Michael Bourn.

On April 29, 2012, Schafer was ejected from a game by umpire Marvin Hudson after disputing an out call on an attempted steal.

On November 1, 2012, the Atlanta Braves reacquired Jordan Schafer from the Houston Astros on waivers. Schafer was placed on the disabled list on July 4, 2013 with a stress fracture in his ankle. He was designated for assignment by the Braves on August 1, 2014.

Schafer was claimed off waivers by the Minnesota Twins on August 3, 2014. He was named the Twins’ 2015 Opening Day center fielder. The team released him on June 18 to make room for an influx of outfield prospects.

Schafer signed a minor league contract with the Los Angeles Dodgers on January 13, 2016. The Dodgers converted him to a pitcher and assigned him to the Double-A Tulsa Drillers of the Texas League. He performed well enough that he was selected to participate in the mid-season Texas League All-Star Game. He pitched in 31 games for Tulsa, six for the Triple-A Oklahoma City Dodgers and another three for the Arizona League Dodgers. Overall, he was 1–1 with a 4.93 ERA in 49 ⁄3 innings.

On December 12, 2016, he signed a minor league contract with the St. Louis Cardinals. He joined the team for spring training, during which, on March 14, 2017, it was announced that Schafer would undergo surgery on his left elbow. He missed the entire season.

Invited to spring training in 2018, he was among six cut to minor-league camp on March 4. He was released on March 12.

On April 3, 2018, Schafer signed a minor league contract with the San Francisco Giants. He was released on June 9, 2018.