Stephen Bratton, who used to co-lead Grace Family Baptist Church in Houston, was arrested on Friday.
Police said in a statement he allegedly began abusing the girl when she was just 13 and continued assaulting her and eventually raping her multiple times a day over a two-year period.
In a statement, the church said Mr Bratton, a father of seven, had confessed to two other pastors last month.
“This activity is wrong according to Biblical and civil law and the church condemns the behaviour as abhorrent,” the statement said.
The same day the pastors found out about the alleged abuse, they filed a police report and have now fired Mr Bratton from his post and excommunicated him from the church.
“The elders have called upon Stephen Bratton to accept the full responsibility for his actions and to place himself at the mercy of the criminal justice system.”
The pastor had made national news in his outspoken support for a bill in the Texas legislature which if passed would have made abortion illegal and charged women with murder if they procured a termination, potentially opening them up to the death penalty.
Mr Bratton spoke in support of the bill at a public hearing in April.
“Whoever authorises or commits murder is guilty,” he said. “They’re guilty already in a court that is far more weighty than what is here in Texas.”
The bill was ultimately blocked by a pro-life conservative Republican state lawmaker, who later had to be provided with additional security by the police after they said they had concerns over his safety.
The other pastors at Grace Family Baptist Church have told local media Mr Bratton first confessed to his wife the day before he spoke with the church leaders.
His wife and seven children are reportedly no longer living with the pastor after a court granted an emergency protection order.
Just last week, the Southern Baptist Church’s annual convention passed several reforms toughening screening processes for Baptist pastors in an effort to tackle a growing scandal about sexual abuse of children within the denomination.
An investigation by the Houston Chronicle and the San Antonio-Express News had found more than 700 people, most of whom were children, were the victims of abuse by Southern Baptist leaders since 1998.