The jihadist group abducted the girls from the town of Dapchi in February.
After their release from captivity and a brief emotional meeting with their parents, the schoolgirls were flown to the capital to meet the president.
The girls - warned by Boko Haram not to return to school - were escorted back to Dapchi by Nigerian soldiers.
As well as meeting President Muhammadu Buhari, the newly-released girls underwent medical and security screenings.
The schoolgirls, who were kidnapped from their boarding school on 19 February, were reportedly released by the side of a road almost five weeks later.
A total of 110 girls were originally kidnapped, but five did not survive the ordeal and one other - a Christian who refused to convert to Islam - is still being held.
"The Buhari administration will not relent in efforts to bring [her] safely back home to her parents," a statement said.
Two other people - a boy and another girl from Dapchi - were freed at the same time, officials also said.
The government denies claims that Boko Haram was paid a ransom for the girls' freedom, or that there was a prisoner swap.
Information Minister Lai Mohammad told the BBC's Focus on Africa that the girls' return was part of ongoing talks about an amnesty in return for a ceasefire.