Pernetti served four years as Rutgers' athletic director before being forced to resign in April for his handling of a scandal involving basketball coach Mike Rice, who verbally abused his players.
The popular Pernetti suspended and fined Rice, also forcing him to undergo anger management. University president Robert Barchi fired Rice after viewing films of the abuse four months later and then forced his athletic director to step down.
Pernetti, who helped to engineer Rutgers' entrance into the Big Ten Conference next season, will bring more than 18 years of business and media experience to his new job. He will oversee all business operations for the team, which is set to start play in 2015.
The club previously hired Claudio Reyna as director of all football operations.