Nikita succumbed to brain cancer on Saturday at TMR International Hospital in Naalya, a Kampala suburb.
Waligwa recovered in 2017 after the treatment, according to BBC, but another tumor was found previous year.
However, in early 2019, Nikita was diagnosed with another brain tumor.
Impressed by her role in the Queen of Katwe movie, hundreds of Ugandans mobilised resources for her treatment on India.
Queen of Katwe star Nikita Pearl Waligwa has passed away on Sunday, according to multiple reports.
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"We are gutted as Gayaza High community", reads the tweet.
Queen of Katwe is a biographical film about child chess prodigy Phiona Mutesi, played by Madina Nalwanga.
"No words can explain the pain at the moment", it added.
The film was received favourably in Uganda, where young people with no acting experience shared the limelight with stars such as Lupita Nyong'o, a Kenyan Oscar-winning actress, and Britain's David Oyelowo.
The 2016 film, which she featured, was based on true story of Phiona Mutesi, who took up chess despite being out of school and went on to compete in worldwide tournaments.