After playing high school basketball in Maine, Miller returned to his home state to attend Purdue University, located in West Lafayette, Indiana, where he played under head coach Gene Keady and assistant coaches Bruce Weber and Frank Kendrick. During his freshman season, along with senior Cuonzo Martin, he led the Boilermakers to a 25–7 record. Along the way, he was part of a Big Ten Conference Title and an NCAA Second Round appearance. He averaged 6.5 points and 5.4 rebounds a game.