Devadas (64) was a pastor of a church at Vadattupura, near Kothamangalam in Ernakulam District.
The pastor took the girl, who had come to the church compound to pluck flowers in July, to his living quarters and molested her, police said.
He also threatened the child that she would be killed if she revealed the incident and later molested her several times.
The incident came to light when the school authorities sent her for counselling, seeing a change in her behaviour.
The Child Welfare Committee recorded her statement recently after which the pastor was arrested yesterday.