She has been called the "dot queen" and has become one of the world's most recognised artists with her psychedelic paintings, sculptures and installations.
According to her company, Kusama died in a hospital in Tokyo on August 14, but news of her death only came on Thursday.
"She continued to paint until her last days, never putting down her brush, and continued to explore eternal love and the eternal soul," a statement from the company said.
Drawings as a salve
Born in 1929 as the youngest daughter in a wealthy but troubled family, Kusama began drawing dots at the age of ten.
"My mother regretted my birth, and I was pushed to my breaking point psychologically," she writes in her autobiography "A Personal History of Polka Dots," according to AFP.
"When I felt sad or lonely, everything became better when I drew pictures."
She had been active as an artist since the 1950s. The characteristically vibrant artworks were an expression of her long struggle with mental illness, AFP writes. In recent years, she created the art from a studio near a psychiatric clinic in Tokyo, where she voluntarily lived for half her life.
Exhibition in Stockholm
"I put dots all over my body and make the surroundings dot-patterned. By creating the same thing over and over again, my existence is buried in art," she writes further in the biography.
The Japanese artist's career has seen a boost in the past decade, largely thanks to the popularity of taking selfies against the backdrop of her colourful art. In 2016, the Moderna Museet in Stockholm held a major, acclaimed retrospective exhibition of her work.
