Lewis entered the West Virginia basketball program after playing just two years of organized basketball. As is often the case with tall teenagers, he grew faster than his coordination grew and it wasn't until his junior year at Huguenot High School that he began to play. Huguenot went 24-19 while he was playing. Junius lettered as a junior and senior while being picked on the honorable mention list for the Virginia All-State team. As a senior, Junius averaged 15.1 points per game while maintaining a 60.0 percent field goal accuracy mark. He grabbed 15.3 rebounds a game and hit on 55 percent of his free throws while he also captained the team.

Lewis was WVU's tallest player since 7-foot Mike Heitz. Going into his freshman year, the coaching staff felt that the one common ingredient needed to compete on the major college level was a big man. Lewis was that "big man." As a sophomore, he played in 26 games and scored a career high nine points against Bucknell, while also scoring seven in the game against Syracuse and six each against St Joe's and Utah. He averaged 3.0 points and 2.6 rebounds that year. Returning for his junior year it was expected that Junius was going to change his style to become more of a finesse player. That year, he came alive in the Eastern Eight tournament, scoring 31 points and grabbing 18 rebounds in three games. He also had 14 points and 9 rebounds against Duquesne in the semi final, followed by 20 points and 10 rebounds against St. Francis (New York) in the championship game. For the season, he played in 28 games averaging 9.8 points and pulling down about 5.9 rebounds per game. Going into his senior year, he had picked up some strength the previous summer. This, combined with his maintained shooting touch, would have enabled him to see some time at the forward spot.