"He shall serve life time rigorous imprisonment," said Judge Saleh Uddin of Dhaka's Women and Children Repression Prevention Tribunal.
The judge also fined Parimal Joydhar Taka 50,000 and ordered six months of added imprisonment in case of a default.
Joydhar, who is in his mid 30's and father of a minor girl, first violated the teenage student of 10th grade in May 2011. He recorded the act on a mobile phone and also blackmailed the girl.
The judge also said he was unhappy with the "flawed" police investigations which made it difficult to prosecute the culprit.
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"Despite the weakness of the police investigation, the allegations against him were proved beyond doubt," the court said.
Joydhar, however, claimed innocence.
"I'm respectful to the law but what else can I say after the honourable judge has pronounced the verdict? I can just say I'm innocent," he said.
The verdict came amid an intensified campaign against sexual harassment of women in Bangladesh particularly in universities and work places.