With a victory over the Fordham Rams in the 2006 Liberty Cup, he became the first Columbia head football coach since Aldo T. "Buff" Donelli in 1957 to win his debut.
It was the first time in a decade that the Lions had finished at .500, and it gave Wilson the highest career winning percentage among Columbia coaches since Charlie Crowley led the team to a 26–16–4 record from 1925 to 1929.
Rutgers had hired Kyle Flood as head coach after the departure of Greg Schiano to the National Football League's Tampa Bay Buccaneers.
In September 2015, Rutgers University officials suspended Flood for three games after an investigation into whether he improperly contacted a professor regarding a player's academic status and athletic eligibility.
On October 10, Rutgers was defeated at home by Michigan State, 31–24, in his final game as interim head coach.