Before competing in the college ranks, Jeffries attended high school at, advancing to the Indiana High School Athletic Association (IHSAA) basketball finals in 2000 before losing to Marion High School, led by current Memphis Grizzlies forward Zach Randolph. In his last two years in high school, one of his teammates was future North Carolina player Sean May. Jeffries was recognized as the 2000 Indiana Mr.
Jeffries played basketball for the Indiana University Hoosiers, where he played for two years before forgoing his junior and senior years to enter the National Basketball Association draft.
Jeffries was a key cog in the Hoosiers" Cinderella run to the 2002 National Collegiate Athletic Association title game. Against #1 Duke in the East Regional Semifinals, Jeffries had 24 points and 15 rebounds to lead Indiana University to a 74-73 upset victory.
Jeffries received the 2002 Silver Basketball from the Chicago Tribune as the Most Valuable Player of the Big Ten.