The incident came to notice after hospital authorities reported the matter to police with the class VIII girl developing complications after the delivery on Monday.
After investigation, police arrested 39-year-old Shibu of Kundara in Kollam district who had been staying with the mother of the victim for the last eight years.
He had allegedly been repeatedly abusing the teenager for the last several months, police said.
He was arrested by police after registering a suo motu case as the victim's parents did not file a complaint.
According to police, the victim did not reveal her harrowing experience to anyone as her stepfather threatened to kill her along with her mother and brother.
The man was produced before the Kollam judicial magistrate and was remanded in judicial custody for two weeks.
Hospital sources said the condition of the girl, who was admitted on September 20, and the child continued to be in complicated state.
