It's understood that the she had been diagnosed with a brain tumour and passed away on Saturday evening (15 February) at TMR International Hospital, in Naalya, Kampala.
Speaking to local media, a family member said Nikita been suffering with a lot of pain before she died.
They said: "The brain was swollen and it is exerting a lot of pressure."
Following Nikita's first diagnosis in 2016, the director of Queen of Katwe Mira Nair attempted to raise money to pay for the actor's treatment in India, after specialists in Uganda revealed they did not have the equipment.
Despite being given the all clear, her tumour later returned and Nikita sadly passed away this weekend.
She was reportedly a student at Gayaza High School at the time of her death.
Fare thee well Nikita Pearl Waligwa. You were a darling to many and we have lost you to brain tumor at such a tender age. Nikita was in S.3. Rest in Perfect Peace dear pic.twitter.com/ny8I9YAjsQ
- Gayaza High School (@gayazahigh) February 16, 2020
The teen shot to fame as the star of Disney movie Queen of Katwe, in which she plays Gloria, a chess prodigy who hailed from the slums of Uganda.
The movie was based on the true story of Phiona Mutesi, who became a star of the chess world, competing in international tournaments.
Since the news of her death was confirmed, social media has been flooded with messages of condolence for Nikita and her family.
Teachers at Gayaza High School wrote: "Fare thee well Nikita Pearl Waligwa. You were a darling to many and we have lost you to brain tumour at such a tender age. Nikita was in S.3. Rest in Perfect Peace dear."
Another user said: "We woke up to the sad news of the passing of Queen of Katwe teen actress, Nikita Pearl Waligwa. It is such a low moment for the country to lose incredible young talent at a tender age. Our sincere condolences to Nikita's family."
"Its so sad to see a country lose such a talented spirit. A what was supposed to be the beginning of a new wave here in Uganda. Rest in Peace dear Nikita Pearl Waligwa. You've been a great inspiration to many Adolescents and Young People and your work shall prevail!" added a third.