The text is divided into five books: the first three are dedicated to the child Emile, the fourth to an exploration of the adolescent, and the fifth to outlining the education of his female counterpart Sophie, as well as to Emile's domestic and civic life.
In Book I, Rousseau discusses not only his fundamental philosophy but also begins to outline how one would have to raise a child to conform with that philosophy. He begins with the early physical and emotional development of the infant and the child.
Emile attempts to "find a way of resolving the contradictions between the natural man who is 'all for himself' and the implications of life in society". The famous opening line does not bode well for the educational project — "Everything is good as it leaves the hands of the Author of things; everything degenerates in the hands of man". But Rousseau acknowledges that every society "must choose between making a man or a citizen" and that the best "social institutions are those that best know how to denature man, to take his absolute existence from him in order to give him a relative one and transport the I into the common unity". To "denature man" for Rousseau is to suppress some of the "natural" instincts that he extols in The Social Contract, published the same year as Emile, but while it might seem that for Rousseau such a process would be entirely negative, this is not so. Emile is not a panegyric for the loss of the noble savage, a term Rousseau never actually used. Instead, it is an effort to explain how natural man can live within society.
Many of Rousseau's suggestions in this book are restatements of the ideas of other educational reformers. For example, he endorses Locke's program of "harden[ing children's] bodies against the intemperance of season, climates, elements; against hunger, thirst, fatigue". He also emphasizes the perils of swaddling and the benefits of mothers nursing their own infants. Rousseau's enthusiasm for breastfeeding led to him to argue: "[B]ut let mothers deign to nurse their children, morals will reform themselves, nature's sentiments will be awakened in every heart, the state will be repeopled" — a hyperbole that demonstrates Rousseau's commitment to grandiose rhetoric. As Peter Jimack, the noted Rousseau scholar, argues: "Rousseau consciously sought to find the striking, lapidary phrase which would compel the attention of his readers and move their hearts, even when it meant, as it often did, an exaggeration of his thought". And, in fact, Rousseau's pronouncements, although not original, effected a revolution in swaddling and breastfeeding.
The second book concerns the initial interactions of the child with the world. Rousseau believed that at this phase education should be derived less from books and more from their interactions with the world, with an emphasis on developing the senses, and the ability to draw inferences from them. Rousseau concludes the chapter with an example of a boy who has been successfully educated through this phase. The father takes the boy out flying kites, and asks the child to infer the position of the kite by looking only at the shadow. This is a task that the child has never specifically been taught, but through inference and understanding of the physical world, the child is able to succeed in his task. In some ways, this approach is the precursor of the Montessori method.
The third book concerns the selection of a trade. Rousseau believed it necessary that the child must be taught a manual skill appropriate to his gender and age, and suitable to his inclinations, by worthy role models.
Once Emile is physically strong and learns to carefully observe the world around him, he is ready for the last part of his education — sentiment: "We have made an active and thinking being. It remains for us, in order to complete the man, only to make a loving and feeling being — that is to say, to perfect reason by sentiment". Emile is a teenager at this point and it is only now that Rousseau believes he is capable of understanding complex human emotions, particularly sympathy. Rousseau argues that the child cannot put himself in the place of others but once adolescence has been reached and he is able do so, Emile can finally be brought into the world and socialized.
In addition to introducing a newly passionate Emile to society during his adolescent years, the tutor also introduces him to religion. According to Rousseau, children cannot understand abstract concepts such as the soul before the age of about fifteen or sixteen, so to introduce religion to them is dangerous. He writes: "It is a lesser evil to be unaware of the divinity than to offend it". Moreover, because children are incapable of understanding the difficult concepts that are part of religion, he points out that children will only recite what is told to them — they are unable to believe.
Book IV also contains the famous "Profession of Faith of the Savoyard Vicar", the section that was largely responsible for the condemnation of Emile and the one, paradoxically, most frequently excerpted and published independently of its parent tome. Rousseau writes at the end of the "Profession": "I have transcribed this writing not as a rule for the sentiments that one ought to follow in religious matters, but as an example of the way one can reason with one’s pupil in order not to diverge from the method I have tried to establish". Rousseau, through the priest, leads his readers through an argument which concludes only to belief in "natural religion": "If he must have another religion", Rousseau writes (that is, beyond a basic "natural religion"), "I no longer have the right to be his guide in that".
In Book V, Rousseau turns to the education of Sophie, Emile's wife-to-be. This brief description of female education sparked an immense contemporary response, perhaps even more so than Emile itself. Mary Wollstonecraft, for example, dedicated a substantial portion of her chapter "Animadversions on Some of the Writers who have Rendered Women Objects of Pity, Bordering on Contempt" in A Vindication of the Rights of Woman (1792) to attacking Rousseau and his arguments. Rousseau begins his description of Sophie, the ideal woman, by describing the differences between men and women in a famous passage:
In what they have in common, they are equal. Where they differ, they are not comparable. A perfect woman and a perfect man ought not to resemble each other in mind any more than in looks, and perfection is not susceptible of more or less. In the union of the sexes each contributes equally to the common aim, but not in the same way. From this diversity arises the first assignable difference in the moral relations of the two sexes.
For Rousseau, "everything man and woman have in common belongs to the species, and ... everything which distinguishes them belongs to the sex". Rousseau states that women should be "passive and weak", "put up little resistance" and are "made specially to please man"; he adds, however, that "man ought to please her in turn", and he explains the dominance of man as a function of "the sole fact of his strength", that is, as a strictly "natural" law, prior to the introduction of "the law of love".
Rousseau also touches on the political upbringing of Emile in book V by including a concise version of his Social Contract in the book. His political treatise The Social Contract was published in the same year as Emile and was likewise soon banned by the government for its controversial theories on general will. The version of this work in Emile, however, does not go into detail concerning the tension between the Sovereign and the Executive, but instead refer the reader to the original work.