Scheppers played shortstop at Dana Hills High School. When his high school team experienced a shortage of pitchers, Scheppers was pressed into action as a pitcher. The Baltimore Orioles drafted Scheppers in the 29th round of the 2005 Major League Baseball Draft, but he opted to attend Fresno State University instead.
Due to an injured rotator cuff and labrum in his shoulder, Scheppers fell in the 2008 Major League Baseball Draft to the second round (48th overall), where he was selected by the Pittsburgh Pirates. Due to health concerns, the Pirates offered Scheppers less money than he was hoping for, and he opted not to sign.
Scheppers signed with the St. Paul Saints of the American Association of Independent Professional Baseball for the 2009 season. Scheppers was chosen in the Supplementary round of the 2009 Major League Baseball Draft 44th overall by the Texas Rangers. Teams passed on him again due to injury concerns, as some believe he has a partially torn labrum, which would require surgery.