He was a standout for Salmen High School in Slidell, Louisiana. After his Senior year, he was drafted in the 21st round (625th overall) of the 1999 MLB Amateur Entry Draft by the Tampa Bay Devil Rays, but chose to attend Louisiana State University on a baseball scholarship instead of going professional.
After his time at LSU, Fontenot was chosen in the first round (19th overall) of the 2001 MLB Amateur Entry Draft by the Baltimore Orioles.
On August 11, 2010, Fontenot was traded to the San Francisco Giants for Evan Crawford.