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.

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