Sills, 25, was indicted by a Guernsey County Common Pleas Court grand jury on one count of rape and one count of kidnapping, both first-degree felonies.
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The police report states that the incident happened on December 5, 2019. It notes that Sills and the victim went to high school together and knew each other for seven or eight years.
It is alleged that on that night, Sills forced the victim to perform sexual acts and held her against her will in a vehicle as he dropped her off at her cousin's house, where the victim said she was staying.
Investigators say the alleged crime was reported immediately, and that a detailed investigation was conducted.
Officials say the case was presented to the grand jury and is being prosecuted by the Special Prosecutions Section of the Attorney General's Office.
Sills, an undrafted free agent who appeared in just one game this season, is a resident of Sarahsville, Ohio.
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The NFL said Sills has been placed on the Commissioner Exempt List, which means for now he may not participate in practices and games or travel with the team.
"The matter will be reviewed under the NFL's personal conduct policy," the league said.
There was no word from the league on how long Sills would be on the list, and whether he would be prevented from participating in Super Bowl LVII.
In a statement, the Eagles said:
"The organization is aware of the legal matter involving Josh Sills. We have been in communication with the league office and are in the process of gathering more information. We have no further comment at this time."
His attorney, Michael Connick, told the Associated Press that the allegations are false and that Sills will be aggressively defended.
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Sills was listed as a backup guard and played just four snaps on special teams against the Cardinals on Oct. 9, the one game he played.
He was on the inactive list for most of the year, including this past Sunday in Philadelphia's conference title victory over the San Francisco 49ers.
Sills spent the first four years of his college career at West Virginia before transferring to Oklahoma State in 2020.
He was one of three undrafted rookies to earn an opening day roster spot for the Eagles' 2022 season.
Sills was issued a summons to appear in Guernsey County Common Pleas Court on Feb. 16, four days after the Eagles are to play the Kansas City Chiefs in the Super Bowl.
The Associated Press contributed to this report.