Waithe won the award for co-writing the "Thanksgiving" episode of "Master of None" with series co-creator and star, Aziz Ansari. Waithe has also had a recurring role on the Netflix comedy.
The critically acclaimed episode was based on her experience of coming out as a lesbian.
In her acceptance speech Waithe called out the importance of diversity in entertainment industry.
"The things that make us different - those are our superpowers," she said,.
She made special mention of her "LGBTQIA family" and urged viewers who feel outside of the mainstream to don a superhero cape every day "and go out there and conquer the world. It would not be as beautiful as it is if we weren't in it."
Waithe is about to launch an autobiographical Showtime series, "The Chi," about her coming of age years in Chicago. She is also developing other TV projects.