The 22-year-old Mendy is accused of engaging in sexual relations with a 16-year-old girl at a campus apartment on Dec. 20. Mendy, from San Jose, California, faces third-degree rape and other charges.
A judge set bail Thursday at $2,000. His attorney did not immediately return a message seeking comment.
Mendy's father told Newsday he could not believe the charges and said he taught his son to make the right choices.
The newspaper reports Mendy is the fourth player from the team to be arrested in the last 10 months.
Stony Brook made its first appearance in the NCAA tournament last year.