Reports have it that Wainaina, who founded the literary magazine Kwani, died after battling a short illness.
Tom Maliti, chairman of the Nairobi-based magazine told The Daily Nation newspaper on Wednesday that the writer passed a few minutes past 10 pm (19:00 GMT) at a Nairobi hospital.
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Wainaina bagged the Caine Prize for African Writing for his short story Discovering Home in 2002. Wainaina revealed he was gay back in 2014.
In 2016, the writer also tweeted that he was HIV-positive. He was listed in Time Magazine in 2014 as one of the Most Influential People in the World.