Schafer was named the Braves' starting center fielder for the 2009 season on April 3, 2009,[4] despite never having played at a higher level than Double-A.[5] 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.[6] He finished the game 2 for 3, with the home run, a single, an intentional walk, and a strikeout.[7]
On June 2, 2009, Schafer was optioned to Triple-A Gwinnett Braves after batting only .204 with 63 strikeouts in 167 at-bats.[8] He was called back up to the major league team on May 24, 2011.[9]
On November 1, 2012, the Atlanta Braves reacquired Schafer from the Astros via waivers.[12] Schafer was placed on the disabled list on July 4, 2013, with a stress fracture in his ankle.[13] In 94 games for Atlanta in 2013, he batted .247/.331/.346 with three home runs, 21 RBI, and 22 stolen bases.
Schafer played in 63 games for the Braves in 2014, hitting .163/.256/.213 with two RBI and 15 stolen bases. He was designated for assignment by the Braves on August 1, 2014.[14]
Schafer was claimed off waivers by the Minnesota Twins on August 3, 2014.[15] He played in 41 games for Minnesota, slashing .285/.345/.362 with one home run, 13 RBI, and 15 stolen bases. Schafer was named the Twins' 2015 Opening Day center fielder. In 27 contests, he hit .217/.250/.261 with no home runs and five RBI. The team released Schafer on June 18 to make room for an influx of outfield prospects.[16]
Schafer signed a minor league contract with the Los Angeles Dodgers on January 13, 2016.[17] The Dodgers converted him to a pitcher and assigned him to the Double-A Tulsa Drillers of the Texas League.[18] He performed well enough that he was selected to participate in the mid-season Texas League All-Star Game.[19] 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 1⁄3 innings.[20] Schafer elected free agency following the season on November 7.[21]
On December 12, 2016, Schafer signed a minor league contract with the St. Louis Cardinals.[22] 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.[23] He missed the entire season.
Invited to spring training in 2018, he was among six cut to minor-league camp on March 4.[24] He was released on March 12.[25]
On April 3, 2018, Schafer signed a minor league contract with the San Francisco Giants.[26] In 7 games for the Triple–A Sacramento River Cats, he compiled a 5.68 ERA with 9 strikeouts across 6+1⁄3 innings pitched. Schafer was released by the Giants organization on June 9.[27]
