In his junior season, Ellis led Kansas in scoring and rebounding with 13.8 points and 6.9 rebounds per game. He shot 45.7 percent from the field and 39.1 percent from behind the arc. Ellis was named to the First Team All-Big 12. He sprained his knee in a late-season game against West Virginia, derailing his season. Ellis considered entering the 2015 NBA draft after the season, but decided to return for his senior year after being told he would be selected in the second round.