Members of the Cherokee Nation and the 2007-2008 President of the American Library Association and American scholar of Indigenous librarianship, Dr. Loriene Roy, Ph.D. (Anishinabe) argue that so-called "Cherokee" words and many customs in The Education of Little Tree are inaccurate. The book has also been criticized on literary grounds. Roy states that "Besides the questions about the author's identity, the book is known for a simplistic plot that used a lot of stereotypical imagery."

Challenged in the Duval County, FL public schools (2015) because a group of parents believed the book was inappropriate for promoting another religion other than Christianity. Story: After the Taliban takes control of an Afghan village they prohibit girls from going to school. Nasreen’s grandmother smuggles her each day to an underground school where she can learn to read and write.