15-year-old Leah Sharibu was among 110 schoolchildren kidnapped in Nigeria by the terrorist group last month.
She has refused to denounce her faith in exchange for her freedom.
Rev Yunusa Nmadu, CEO of Christian Solidarity Worldwide (CSW) in Nigeria told Premier why the girls were targeted.
"Boko Haram itself means Western education is forbidden so they do everything possible so that they can scare away school-aged children from going to school - especially the girl child," he said.
The Nigerian government reached a deal with Boko Haram in the early hours of 21st March.
The terrorist organistaion - which has links to the Islamic State - drove into Dapchi with nine trucks and unloaded all of the girls, except the five that died during the kidnaping, and Sharibu.
However, Dr Khataza Gondwe from CSW told Premier mistakes were made by the army when the girls were kidnapped.
She claimed: "On the day the girls were abducted, the army received messages that Boko Haram was on the move towards Dapchi and the army actually moved out of Dapchi and didn't come back despite repeated messages being sent."
Sharibu's mother told local reporters that her daughter's friends said Boko Haram "tried to convince her but she said she will not convert to Islam."
She added: "Boko Haram said since she will not convert to Islam she should remain behind.
"That was how they left her."
CSW urged Christians to pray for Sharibu, just as the youngster had asked her departing Muslim classmates to do for her as well.
Listen to Rev Yunusa Nmadu and Dr Khataza Gondwe speaking with Premier's Rick Easter:
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