Coming to Nebraska as freshman for the 1988 season, Benjamin made an impact early. He was named to Baseball America's first-team Freshman All-America squad and earned second-team All-Big Eight honors. Benjamin started all 71 games in left field and set school records for home runs (21) and walks drawn (91) in a season. His 91 walks were also the leading mark in the nation for the 1988 season. Benjamin led the team with 141 total bases while hitting .288 with 78 RBIs, 12 doubles and 18 stolen bases.
In his sophomore campaign, Benjamin again led the team in home runs and walks with nine and 66, respectively. He batted .253 with 56 runs scored, 46 hits, seven doubles and 18 stolen bases while starting all 58 games in left field. He was able to draw at least one walk in 40 of the 58 games.
Benjamin finished his time at Nebraska with a career year, hitting .335 on his way to first-team All-Big Eight honors. He led the team in RBIs (73), runs scored (61), home runs (18) and walks drawn (66), while both his home run and RBI totals ranked him second in the Big Eight. His career 48 home runs and 223 walks were both the most of any player in Nebraska history at the time of his graduation.