Miller's junior season showed more progress than the prior season, averaging 14.3 points and 8.3 rebounds a game. Finishing second in the conference, Miller, along with teammate and former NBA player Brian Cardinal, helped the Boilers to a third straight NCAA Second Round finish. They beat Rhode Island in overtime, where Brad scored 31 points, grabbed eight rebounds and set a school tournament record with made/attempted free throws, going 15–21 from the line. He finished his junior season with an 18–12 record. Throughout his junior year, Miller became the only center in Purdue history to lead the team in assists.