The region, which takes in parts of Nigeria, Niger, Chad and Cameroon, is suffering from a long-running Islamist insurgency led by Boko Haram as well as the climate change-induced shrinking of a lake that once sustained millions.
More than a third of girls surveyed by child rights group Plan International said they felt unsafe at home, while more than a fifth had been beaten by teenage boys, teachers or family members in the past month.
Many of the girls were forced into early marriages or transactional sex, and over a tenth had been pregnant, according to the results, released as aid agencies, governments and donors met in Berlin on Monday to discuss the conflict.
"I think the striking part is the feeling of helplessness from these girls," said Hussaini Abdu, Plan International's Nigeria country director.
"They are extremely afraid of the militants and even at the domestic level they are not feeling safe," he told the Thomson Reuters Foundation.
Plan International chose to focus on adolescent girls because their needs are often neglected in humanitarian response plans, he said.
Many girls have missed out on school because of the conflict, leaving them with few skills for employment, said Salamatu Kemokai, a policy specialist in Nigeria for UN Women, the United Nations agency for gender equality.
As a result, a man who will provide food or security in exchange for sex is often welcomed, she said.
"The sad part of it is that some of them do not even see it as exploitation," she told the Thomson Reuters Foundation.
Plan International surveyed 449 girls aged between 10 and 19 in conflict-hit parts of Cameroon, Niger and Nigeria.
Many said they wished they could attend school or learn a trade and that they wanted more information about sex and reproduction.
"This report is important not only for Nigeria but for every humanitarian situation. The contexts differ but in most cases the realities of adolescent girls are the same," Abdu said.
Boko Haram's fight to establish an Islamic state in the region has killed thousands and displaced millions more.
Aid agencies say the Boko Haram insurgency and the shrinking of Lake Chad have created one of the world's most neglected crises with about 11 million people dependent on aid.