The book has been at the center of several controversies regarding the depiction of sex and violence in books written for young adults. Alexie responded to such complaints in a 2011 Wall Street Journal post entitled "Why the Best Kids Books Are Written in Blood", in which he argues that attempts to prevent school-aged children from learning about the harsher aspects of contemporary life are "way, way too late". He uses his own life as an example:
Of course, all during my childhood, would-be saviors tried to rescue my fellow tribal members. They wanted to rescue me. But, even then, I could only laugh at their platitudes. In those days, the cultural conservatives thought that KISS and Black Sabbath were going to impede my moral development. They wanted to protect me from sex when I had already been raped. They wanted to protect me from evil though a future serial killer had already abused me. They wanted me to profess my love for God without considering that I was the child and grandchild of men and women who’d been sexually and physically abused by generations of clergy.
Alexie also points out in that post that he has visited many classrooms and received many letters and messages from students who liked the book, noting that these students have had difficult experiences similar to his own—"depression, attempted suicide, gang warfare, sexual and physical abuse, absentee parents, poverty, racism, and learning disabilities"—and he notes:
I have yet to receive a letter from a child somehow debilitated by the domestic violence, drug abuse, racism, poverty, sexuality, and murder contained in my book. To the contrary, kids as young as ten have sent me autobiographical letters written in crayon, complete with drawings inspired by my book, that are just as dark, terrifying, and redemptive as anything I’ve ever read.
In April 2010, the Stockton School Board, located in Missouri, voted to remove The Absolutely True Diary of a Part-Time Indian from the school library after a parent complained about its content. The American Library Association has asked the school board to reconsider its decision. In September 2010 the School Board decided to uphold its April decision to ban the book from the curriculum and from the library with a vote of 5–2.
In June 2011, the Richland School Board, in Washington, voted to prohibit the use of The Absolutely True Diary of a Part-Time Indian for all grade levels. The book was subject to a pilot program, by a ninth-grade English class, prior to an Instructional Materials Committee review. Although the original vote was only about the appropriateness of the novel for freshman English students, the Committee decided to remove it from all grades, by a vote of 3–2. At the time of the ban, all 10 copies of the novel at the Richland Library were checked out and the same 10 copies had holds. The decision to ban the novel was reversed the following month after some of the board members and district committee members actually read the novel stating that they found the novel to be "outstanding".
In mid-October 2010, Newcastle Middle School attempted to use the book in the 8th grade English curriculum. At first, the district allowed it under the premise that children who were not allowed to read it would bring a signed paper allowing them to read the alternate book Tangerine. About two weeks after the announcement made to the 8th graders, the school board banned it on terms of teaching it in a curriculum, but still allowed it in the library for those who wished to read it.
In April 2014, the book was pulled from the Meridian district’s supplemental reading list after significant parental disapproval of the subject matter of the novel. The book had been a part of its curriculum since 2010. Students protested to remove the ban but were unsuccessful. The National Coalition Against Censorship states that The Absolutely True Diary of a Part-Time Indian is its most frequently defended title.