In 1990 she received the Catholic Library Association's Regina Medal, given annually 'for continued, distinguished contribution to children's literature'. Hamilton was awarded the Hans Christian Andersen Award for Writing (the highest international recognition bestowed on an author or illustrator of children's literature), the Laura Ingalls Wilder Award (which is now known as the Children's Literature Legacy Award) and the University of Southern Mississippi de Grummond Medal. In 2021, the Library of America published a volume collecting five of her novels. Her novel The Planet of Junior Brown was adapted for the 1997 film The Planet of Junior Brown, directed by Clement Virgo. The Virginia Hamilton Conference on Multicultural Literature for Youth has been held at Kent State University each year since 1984. In 1979, the Supersisters trading card set was produced and distributed one of the cards featured Hamilton's name and picture. Three books have been published posthumously: Bruh Rabbit and the Tar Baby Girl (2003), Wee Winnie Witch's Skinny (2004), and Virginia Hamilton: Speeches, Essays, and Conversations, edited by Arnold Adoff and Kacy Cook (2010). Hamilton died of breast cancer on February 19, 2002, in Dayton, Ohio, aged 65. The book also won the National Book Award, the Lewis Carroll Shelf Award, the Boston Globe–Horn Book Award and The New York Times Outstanding Children's Book of the Year. Higgins, the Great (1974) won the Newbery Medal, making Hamilton the first black author to receive the medal. Hamilton published The Planet of Junior Brown, which was named a Newbery Honor Book and also won the Lewis Carroll Shelf Award in 1971.

Zeely was named an American Library Association Notable Book and won the Nancy Bloch Award. In 1967, Zeely was published, the first of more than 40 books.

Adoff supported the family by working as a teacher, so Hamilton spent her time writing and had two children. The two later returned with their children to live on the farm where Hamilton was raised. She met poet Arnold Adoff while living in New York City, and married him in 1960.

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