According to Ugandan reports, the young star died at a hospital in Naalya, Kampala, last night.
She was initially diagnosed with the tumor in 2016, and she made a recovery in 2017.
Queen of Katwe director Mira Nair helped organise efforts to fund Waligwa's treatment during filming, according to BBC.
Nikita Pearl Waligwa, as Gloria in Queen of Katwe. You were a darling to many and we have lost you to brain tumor at such a tender age.
Waligwa had been diagnosed with a brain tumour.
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Waligwa was a senior at Gayaza High School, who commented on her untimely death via Twitter.
Waligwa starred alongside Lupita Nyong'o and David Oyelowo in the film, which told the real-life story of Phiona Mutesi, a young girl living in the Ugandan slum of Katwe who became a chess champion.
Nikita starred as Gloria, Phiona's best friend who taught her how to play chess.
Queen of Katwe is a biographical film about child chess prodigy Phiona Mutesi, played by Madina Nalwanga.