Henry was charged with trying to have sexual contact with a 15-year-old girl. Sexual misconduct covers any attempt of sexual contact between an adult and someone younger than 17.
In agreeing to charge the 22-year-old Henry with a misdemeanor, District Attorney Frank Clark acknowledged that the sexual encounter was consensual, and that the girl told Henry she was almost 18.
Along with the 90 days in jail, Henry can be fined a maximum $500 for the misdemeanor.
The guilty plea could lead to a suspension by the NFL for violating the league's personal conduct policy.
The Bills issued no statement on Henry's guilty plea.
A second-round pick out of Tennessee, Henry won the starting halfback job over Shawn Bryson and Sammy Morris in the preseason and has rushed for 303 yards on 97 carries in five games.