Additional District and Session Court judge Aminur Rahman on Friday found the accused guilty under Section 6 of POCSO Act and handed him the life sentence, besides slapping a fine of Rs 2,000 on him.
The judge also directed the District Legal Service Authority to pay a compensation of Rs 5 lakh to the victim, said special public prosecutor, Manashjyoti Neog.
The nine-year-old girl was regularly raped by her father for two years after the death of her mother.
The incident came to light when the victim fled her residence on April 24, 2017 and narrated her agony to two nurses at a government hospital here.
The nurses, in turn, contacted the Child Line which rescued the girl and lodged a complaint at the Morikolong Police Outpost.
The case was transferred to Nagaon Sadar Police Station which submitted the charge sheet in 37 days, a police officer said.