Multiple reports, including media from her native Uganda, state that Waligwa suffered from a brain tumor.
She was reportedly diagnosed with a brain tumor in 2016 and received an all-clear in 2017 before another tumor was discovered last year.
Waligwa's body was taken to a cathedral for a funeral service today, according to the reports, and will be buried on Monday.
"Queen of Katwe" tells the story of a young Ugandan chess prodigy named Phiona Mutesi. Waligwa starred as a friend of Mutesi.
Lupita Nyong'o and David Oyelowo also starred in the film.
Oyelowo, 43, took to Instagram to share his grief over losing his co-star.
"We mourn the loss of our beautiful Nikita Pearl Waligwa," he wrote. "She was a ball of light in @queenofkatwemovie and in life. Her battle with a brain tumor was humbling to witness. Her light will live on."
The post contained a photo of Waligwa in character, holding up two chess pieces. A quote from her character was also featured in the image, reading: "In chess, the small one can become the big one."