Scott, 23, was booked Sunday afternoon at the Ascension Parish Jail, the sheriff's office said. Bond had not been set as of late Sunday afternoon and it was not immediately known if he has an attorney.
Sheriff's spokesman Tony Bacala told The Advocate newspaper that deputies responded to Scott's home in the Baton Rouge suburb of Prairieville about 4 a.m. after someone reported a disturbance there.
He said the disturbance was the result of "an 18-year old alleging she was raped by Charles Edward Scott Jr." No further details were available.
Scott, whose father played football at the Air Force Academy, graduated from LSU with 2,317 yards rushing. He was drafted in 2010 by the Philadelphia Eagles, who traded him to Arizona for another sixth-round pick. The Cardinals cut him in September 2010.
When he was named Louisiana's Mr. Football in December 2005, Scott was described as humble, mild-mannered and the pride of Shady Grove Baptist Church.
Calls to the homes of Scott's father and his high-school coach, and to LSU sports information director Michael Bonnette were not immediately returned.