Berry played prep baseball at Morse High School in San Diego, California, where he also played football and basketball. He was a classmate and teammate of current Baltimore Orioles outfielder Adam Jones, and the two remain good friends.

Berry played one season of baseball at Grossmont Junior College before moving on to San Diego State University (SDSU). Berry's head coach at SDSU was former major leaguer and Baseball Hall of Fame member Tony Gwynn. He was named to the All-Mountain West Conference first team in 2005 and the second team in 2006.

Berry was originally drafted by the Atlanta Braves in the 25th round of the 2003 Major League Baseball Draft out of high school, but did not sign. He was drafted three years later in the fifth round of the 2006 Major League Baseball Draft by the Philadelphia Phillies, with whom he signed within 48 hours.