In the mid-1970s, South Carolina State University, a program located in Orangeburg, South Carolina and very near Wilson's hometown, discontinued its baseball program just days after Wilson had signed a letter of intent to play for the Bulldogs. As a result, Mookie attended Spartanburg Methodist College for the 1974 & 1975 seasons. While attending Spartanburg Methodist, Mookie was drafted by the Los Angeles Dodgers in the fourth round of the January 1976 amateur draft but he did not sign. Instead, Mookie transferred to play for The University of South Carolina Gamecocks, preferring to attempt to better his draft stock by playing for former New York Yankees great and fellow South Carolina native Bobby Richardson who was the head coach of the Gamecocks at the time. The gamble paid off as Wilson was selected in the second round of the 1977 Major League Baseball draft by the New York Mets. Mookie was part of the Gamecocks' second team to play for a national championship in Omaha, Nebraska in the 1977 College World Series. He was also named to the 1977 All-Tournament team as an outfielder. He earned a B. S. degree from Mercy College.