Abul Sheikh had been absconding since the girl's half nude body was found near a canal not far from her home on October 27.
Based on complaints filed by the girl's family and by neighbours, the police had been on the lookout for Abul who had fled to Kerala.
Acting on a tip-off that the accused was returning to Nababhat secretly to contact lawyers, police caught him as soon as he disembarked from a bus, police said.
The Class XII girl went missing on October 25 after she left home for her tuition class in the evening. Her family had filed a police complaint the next day and her body was found the morning after.
On interrogating them, the police arrested three others, while three others, including Abul fled.
Abul was named the prime accused both by the family and the neighbours, police added.