DPS arrested Alan Bailey on Tuesday, but officials with the football league didn't know about the charges until Thursday.
League president Anthony Williams said Bailey turned in his resignation Thursday afternoon.
"I'm just saddened to hear this," Williams said.
Bailey was charged with one count of sexual assault of a child and two counts of indecency with a child. According to jail records, the charges stem from incidents in 2003 and 2006.
"We're all stunned. These are very serious allegations," Williams said.
The football league runs a criminal background check each season for all volunteers. Williams released a statement that reads in part: "If throughout the season the league is notified and can confirm any inappropriate behavior, the volunteer is immediately removed from the position until a complete investigation has been conducted."
Many parents voiced concerns after hearing about Bailey's arrest, but Williams emphasized the safety of children in the league is their top priority.
"The whole intent of youth sports is to motivate, encourage and inspire youth. If these allegations are true, we will react accordingly," he said.
Bailey was released from the Taylor County Jail the same day he was booked on a $35,000 bond.
The league offers football and cheerleading programs for children from preschool through sixth grade. There are nearly 1,200 children signed up this year.