She was among 83 teenagers who Boko Haram jihadists had agreed to release at the weekend but only 82 came back, said a spokesman for Nigerian president Muhammadu Buhari.
Garba Shehu said: “One of the girls refused to join the released girls. She said ‘I am happy where I am. I have a husband.'”
The other 82 were freed on Saturday in exchange for five Boko Haram commanders after months of negotiations which also involved the Red Cross and Swiss government.
The girls are now in the capital Abuja being looked after by government officials as they try to adjust back into society.
Mr Shehu said authorities were working to check their identities so they can be reunited with their families.
More than 200 schoolgirls were originally kidnapped by the militants from the town of Chibok in April 2014. Some 113 are still in captivity.
Girls who escaped soon afterwards claimed some classmates had died from illness while others did not want to come home because they had been radicalised by the insurgents.
Elizabeth Pearson, a Boko Haram expert, said the case of the Chibok girl who refused to leave was “likely to be quite prevalent”.
She said: “From what we know of other young women who’ve returned, the relationships with their captors is very complex and at times quite ambiguous.
“We assume because they are abducted they are therefore likely to resist their captors. In fact they have to develop relationships of some sort in order to survive.”
Human rights activists also fear some of the girls have been used by Boko Haram to carry out suicide bombings as part of the group’s insurgency.
The first group of 21 Chibok girls, who were freed in October, have been in government care, receiving medical attention, trauma counselling and rehabilitation.
Three had previously been found or escaped.
Talks are understood to have started to free all or some of the remaining 113.