Christie's said the painting of Malala Yousafzai by Jonathan Yeo sold for $102,500, including the buyer's premium.
Yeo painted Yousafzai in 2013 after she started attending a school in Birmingham, England, where she now lives.
The sale proceeds will go to the Malala Fund charity. The fund said the money would in turn be given to Nigerian nonprofits that focus on education for women and girls in the wake of the kidnapping of more than 300 schoolgirls in that country.
The painting hung in the National Portrait Gallery in London last year for an exhibition of Yeo's portraits of well-known figures, including Sienna Miller, Kevin Spacey and Rupert Murdoch.
Malala was 15 when she was shot in 2012 as she traveled to her Pakistani school. President Barack Obama has called her the "bravest girl in the world."
In an interview last week, Yeo said he wanted the portrait to capture "this extraordinary dichotomy" of someone with "enormous power and wisdom" but who is still very young.
"Her birth instinct isn't self-pity but rather what else she could do to help other girls in her position," Yeo said.
He said he spent "a lot of time chatting" with her and "hearing her world views and what her life is like" before sitting down to paint her.
Yeo, whose works are also in the Royal Collection, said he depicted her doing homework to reflect the irony that "the simple everyday thing she's doing was what created the cataclysmic change in her life that nearly killed her."
When the portrait was finished, Yeo said, Malala told him "it's how she sees herself."