John Holt was the oldest of three children, and raised in the New England region of the USA. He was sent to private schools, whose names he declined to reveal. He said, "... the things I'm supposed to know so much about I never learned in schools." After graduating from university, Holt joined the United States Navy and served on board the USS Barbero, a submarine that fought in the Pacific Ocean. During the war, he concluded that nuclear weapons were the world's greatest danger, and only a world government could prevent nuclear war. After his three-year tour of duty in the Navy, he got a job with the New York branch of the United World Federalists. Starting in the mail room, he became the executive director of the New York branch within six years. However, he became frustrated with UWF's ineffectiveness and left it in 1952.

At the urging of his sister, Holt became a fifth grade teacher. He also spent much time with the babies and young children of his sisters and friends. He was struck by the difference between the 10s (whom he liked) and the 1s and 2s. The children in the classroom, despite their rich backgrounds and high IQs, were, with few exceptions, frightened, timid, evasive, and self-protecting. The infants at home were bold adventurers. After several years of teaching in Colorado, he moved to Boston. It was here that he met Bill Hull, a fellow teacher, and they decided to start a classroom observation project; one would teach, while the other would watch. The notes and journal entries Holt accumulated during his first eleven years of teaching formed the core of two of his most popular books How Children Fail and How Children Learn, as well as his lesser-known and more radical work, The Rights and Needs of Children. These three books detailed the foundational ideas of Holt's philosophy of education. He held that the primary reason children did not learn in schools was fear: fear of getting the wrong answers, fear of being ridiculed by the teacher and classmates, fear of not being good enough. He maintained that this was made worse by children being forced to study things that they were not necessarily interested in.

In 1964 Holt published his first book, How Children Fail, asserting that the academic failure of schoolchildren was not despite the efforts of the schools, but actually because of the schools. Not surprisingly, How Children Fail ignited a firestorm of controversy. Holt was catapulted into the American national consciousness to the extent that he made appearances on major TV talk shows, wrote book reviews for Life magazine, and was a guest on the To Tell The Truth TV game show. In his follow-up work, How Children Learn, published in 1967, Holt tried to elucidate the learning process of children and why he believed school short circuits that process.

Holt became a sought-after speaker and supporter of school reform. He was a visiting teacher for the education departments at Harvard University and the University of California, Berkeley.Up to this time, no book of his suggested any alternative to institutional schooling; he had hoped to initiate a profound rethinking of education to make schools friendlier for children. But as the years passed, he became convinced that the way schools were was what society wanted, and that a serious reexamination was not going to happen in his lifetime.

Holt then ended his teaching career in order to publicize his ideas about education full time. He soon encountered books by other authors questioning the premises and efficacy of compulsory schooling, including Deschooling Society by Ivan Illich (1970) and No More Public School by Harold Bennet (1972). (Bennet went so far as to offer advice to parents on how to keep their children out of school illegally.) In 1976, he published Instead of Education: Ways to Help People Do Things Better, whose conclusion called for a "Children's Underground Railroad" to help children escape compulsory schooling. Readers of this book contacted Holt, saying that they were educating their children at home. After corresponding with a number of these families, Holt began a newsletter in 1977, dedicated to home education, Growing Without Schooling.

Holt's philosophy was simple:

"... the human animal is a learning animal; we like to learn; we are good at it; we don't need to be shown how or made to do it. What kills the processes are the people interfering with it or trying to regulate it or control it."

It was no great leap from there to arrive at homeschooling. In 1980, Holt said:

"I want to make it clear that I don’t see homeschooling as some kind of answer to badness of schools. I think that the home is the proper base for the exploration of the world which we call learning or education. Home would be the best base no matter how good the schools were."

In his 40th year, Holt began to study the cello, an experience he wrote about in his 1979 book My Musical Life Story.

Holt continued to advocate for expansive reform of education until his 1985 death.

After many years of working within the school system, Holt became disillusioned with it. He became convinced that reform of the school system was not possible because it was fundamentally flawed, and began to advocate homeschooling. However, it would be pointless to simply remove children from the school environment, if parents simply recreated that environment at home. Holt believed that children did not need to be coerced into learning; they would do so naturally if given the freedom to follow their own interests and a rich assortment of resources. This line of thought came to be called unschooling.

Holt's Growing Without Schooling (GWS), founded in 1977, was the nation's first home education newsletter. He also set up John Holt's Bookstore, which made selected books available by mail order. This brought in additional revenue that helped sustain the newsletter, which carried very little advertising.

Holt's sole book on homeschooling, Teach Your Own, was published in 1981. It quickly became the "Bible" of the early homeschooling movement. It was revised by his colleague, Patrick Farenga, and republished in 2003 by Perseus Books.

In addition to home schooling, Holt also espoused many of the principles now taken up by the youth rights movement, including eliminating the voting age, and allowing young people to sign contracts and obtain employment.

Holt wrote 10 books that have greatly influenced the unschooling movements. His writings have influenced many individuals and organizations, including The Evergreen State College, Caleb Gattegno, Americans for a Society Free from Age Restrictions, the National Youth Rights Association, and The Freechild Project.