A 6'8" (2.03 m), 225 lb (102 kg) center, Wilson starred at Marshall High School in Chicago, Illinois. He led the Commandos to four straight appearances in the Chicago Public League, and they won Illinois state championships in 1958 and 1960.

As a senior, he was named a high school All-American after three seasons of averaging 25, 27, and 26 points per game, and in 1960 he was the inaugural winner of the Chicago Sun-Times Player of the Year award. Wilson was named All-State three years.

Recruited by many colleges, he chose to attend the University of Cincinnati primarily because of his admiration of Bearcats' star Oscar Robertson. As a sophomore in his first year on the varsity in 1961–62, he broke into the starting lineup for Ed Jucker's Bearcats in the 14th game, and for the season he averaged 9.2 points per game. The Bearcats were co-champions of the Missouri Valley Conference (MVC) and posted a record of 29-2, capping off the season by winning the NCAA championship game over Ohio State 71-59, the Bearcats' second consecutive national title.

As a junior in 1962–63, Wilson led the Bearcats with 11.2 rebounds per game, a .505 field goal percentage. and 1.4 blocked shots to go with 15.0 points per game. He was named All-MVC, and he was named second-team All-American by The Sporting News and Converse. The Bearcats went 26-2, again won the MVC and advanced to the NCAA championship game for the third consecutive season, but they were beaten by Loyola University Chicago in overtime, 60-58.

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