Martin Dysart is a psychiatrist in a mental hospital. He begins with a monologue in which he outlines the case of 17-year-old Alan Strang. He also divulges his feeling that his occupation is not all that he wishes it to be and his feelings of dissatisfaction and disappointment about his barren life. Dysart finds that there is a never-ending supply of troubled young people for him to "adjust" back into "normal" living; but he doubts the value of treating these youths, since they will simply return to a dull, normal life that lacks any commitment and "worship" (a recurring theme). He comments that Alan Strang's crime was extreme but adds that just such extremity is needed to break free from the chains of existence.
A court magistrate, Hesther Saloman, visits Dysart, believing that he has the skills to help Alan come to terms with his violent acts involving six horses. At the hospital, Dysart has a great deal of difficulty making any kind of headway with Alan, who at first responds to questioning by singing TV advertising jingles.
Dysart reveals a dream he has had, in a Grecian/Homeric setting, in which he is a public official presiding over a mass ritual sacrifice. Dysart slices open the viscera of hundreds of children, and pulls out their entrails. He becomes disgusted with what he is doing, but desiring to "look professional" to the other officials, does not stop.
Dysart interviews Alan's parents. He learns that, from an early age, Alan has been receiving conflicting viewpoints on religion from his parents. Alan's mother, Dora Strang, is a devout Christian who has read to him daily from the Bible. This practice has antagonized Alan's atheist father, Frank Strang.
Slowly, Dysart makes contact with Alan by playing a game where each of them asks a question, which must be answered honestly.
Dysart learns that Frank, concerned that Alan has taken far too much interest in the more violent aspects of the Bible, destroyed a violent picture of the Crucifixion that Alan had hung at the foot of his bed. Alan replaced the picture with one of a horse, with large, staring eyes.
Alan reveals to Dysart that during his youth, he had established his attraction to horses by way of his mother's biblical tales, a horse story that she had read to him, western movies, and his grandfather's interest in horses and riding. Alan's sexual training began with his mother who told him he could find true love and contentment by way of religious devotion and marriage. During this time Alan also begins to show a sexual attraction to horses, desiring to pet their thick coats, feel their muscular bodies and smell their sweat. Alan reveals to Dysart that he had first encountered a horse at age six, on the beach. A rider approached him, and took him up on the horse. Alan was visibly excited, but his parents found him and his father pulled him violently off the horse. The horse rider scoffed at the father and rode off.
In another key scene, Dysart hypnotizes Alan, and during the hypnosis, Dysart reveals elements of his terrifying dream of the ritual murder of children. Dysart begins to jog Alan's memory by filling in blanks, and asking questions. Alan reveals that he wants to help the horses by removing the bit, which enslaves them.
After turning 17, Alan took a job working in a shop selling electrical goods, where he met Jill Mason, an outgoing and free-spirited young woman. She visits the shop wanting to purchase blades for horse-clippers. Alan was instantly interested when he discovered that Jill has such close contact with horses after she tells him that she works for a local stable owner. Jill suggested that Alan work for the owner of the stables, Harry Dalton, and Alan agrees.
Dysart meets with Dalton who tells him that he first held Alan to be a model worker, since he kept the stables immaculately clean and grooms the horses, including one named "Nugget." Through Dysart's questioning, it becomes clear that Alan is erotically fixated on Nugget (or 'Equus') and secretly takes him for midnight rides, bareback and naked. Alan also envisions himself as a king, on the godhead Equus, both destroying their enemies.
Dysart gives Alan a placebo "truth pill". Revealing a tryst with Jill, he begins to re-enact the event. Jill, who had taken an interest in Alan, had asked him to take her to a porno theater. While there, they both ran into Frank. Alan was traumatized, particularly when he realized that his father was lying when he tried to justify his presence in the theater. However, this occurrence allows Alan to realize that sex is a natural thing for all men... even his father. Alan walks Jill home after they leave. She convinces Alan to come to the stables with her.
Once there, Jill seduces Alan and the two start having sex. However, Alan breaks this off when he hears the horses making noises in the stables beneath. Jill tries to ask Alan what the problem is, but he shouts at her to leave. After Jill dresses and walks out of the stables, the still nude Alan begs the horses for forgiveness for having pre-marital sex, as he sees the horses as God-like figures. "Mine!...You're mine!...I am yours and you are mine!" cries Equus through Dysart's voice, but then he becomes threatening: "The Lord thy God is a jealous God," Equus/Dysart seethes, "He sees you, he sees you forever and ever, Alan. He sees you!...He sees you!" Alan screams, "God sees!" and then he says "No more. No more, Equus!" Alan then blinds the six horses in the stable with a steel spike, whose eyes have "seen" his very soul.
The final scene has another monologue by Dysart questioning the fundamentals of his practice and whether or not what he does will actually help Alan, as the effect of his treatment will remove Alan's humanity which includes his intense sexual and religious commitment, and his worship of the horses as well.