The Kite Runner is the story of Amir and Hassan, two boys in pre-Soviet Afghanistan. Amir is the son of a wealthy merchant, Hassan a servant. The two have an uneven friendship. Hassan is secretly Amir's half-brother, a product of his father's indiscretion with a servant. The two grow apart during the war and the subsequent rise of the Taliban and Amir journeys to America where his father passes away. He returns to Afghanistan to claim Hassan's son in the wake of Hassan's death at the hands of the Taliban.
Amir, a well-to-do Pashtun boy, and Hassan, a Hazara and the son of Amir's father's servant, Ali, spend their days in a peaceful Kabul, kite fighting, roaming the streets and being boys. Amir’s father (who is generally referred to as Baba, "daddy", throughout the book) loves both the boys, but seems critical of Amir for not being manly enough. Amir also fears his father blames him for his mother’s death during childbirth. However, he has a kind father figure in the form of Rahim Khan, Baba’s friend, who understands Amir better, and is supportive of his interest in writing stories.
Assef, a notoriously mean and violent older boy with sadistic tendencies, blames Amir for socializing with a Hazara, according to Assef an inferior race that should only live in Hazarajat. He prepares to attack Amir with his steel knuckles, but Hassan bravely stands up to him, threatening to shoot Assef in the eye with his slingshot. Assef and his henchmen back off, but Assef says he will take revenge.
Hassan is a successful "kite runner" for Amir, knowing where the kite will land without even watching it. One triumphant day, Amir wins the local tournament, and finally Baba's praise. Hassan goes to run the last cut kite, a great trophy, for Amir saying "For you, a thousand times over." Unfortunately, Hassan runs into Assef and his two henchmen. Hassan refuses to give up Amir's kite, so Assef exacts his revenge, assaulting and raping him. Wondering why Hassan is taking so long, Amir searches for Hassan and hides when he hears Assef's voice. He witnesses the rape but is too scared to help him. Afterwards, for some time Hassan and Amir keep a distance from each other. Amir reacts indifferently because he feels ashamed, and is frustrated by Hassan's saint-like behavior. Already jealous of Baba's love for Hassan, he worries if Baba knew how bravely Hassan defended Amir's kite, and how cowardly Amir acted, that Baba's love for Hassan would grow even more.
To force Hassan to leave, Amir frames him as a thief, and Hassan falsely confesses. Baba forgives him, despite the fact that, as he explained earlier, he believes that "there is no act more wretched than stealing." Hassan and his father Ali, to Baba's extreme sorrow, leave anyway. Hassan's departure frees Amir of the daily reminder of his cowardice and betrayal, but he still lives in their shadow and his guilt.
Five years later, the Russians invade Afghanistan; Amir and Baba escape to Peshawar, Pakistan and then to Fremont, California, where Amir and Baba, who lived in luxury in an expansive mansion in Afghanistan, settle in a run-down apartment and Baba begins work at a gas station. Amir eventually takes classes at a local community college to develop his writing skills. Every Sunday, Baba and Amir make extra money selling used goods at a flea market in San Jose. There, Amir meets fellow refugee Soraya Taheri and her family; Soraya's father, who was a high-ranking officer in Afghanistan, has contempt of Amir's literary aspiration. Baba is diagnosed with terminal oat cell carcinoma but is still capable of granting Amir one last favor: he asks Soraya's father's permission for Amir to marry her. He agrees and the two marry. Shortly thereafter Baba dies. Amir and Soraya learn that they cannot have children.
Amir embarks on a successful career as a novelist. Fifteen years after his wedding, Amir receives a call from Rahim Khan, who is dying from an illness. Rahim Khan asks Amir to come to Pakistan. He enigmatically tells Amir "there is a way to be good again." Amir goes.
From Rahim Khan, Amir learns the fates of Ali and Hassan. Ali was killed by a land mine. Hassan had a wife and a son, named Sohrab, and had returned to Baba’s house as a caretaker at Rahim Khan’s request. One day the Taliban ordered him to give it up and leave, but he refused, and was murdered, along with his wife. Rahim Khan reveals that Ali was not really Hassan's father. Hassan was actually the son of Baba, therefore Amir's half-brother. Finally, Rahim Khan tells Amir that the true reason he has called Amir to Pakistan is to go to Kabul to rescue Hassan's son, Sohrab, from an orphanage.
Amir returns to Taliban-controlled Kabul with a guide, Farid, and searches for Sohrab at the orphanage. In order to enter Taliban territory, Amir, who is normally clean shaven, dons a fake beard and mustache, because otherwise the Taliban would exact Shariah punishment against him. However, he does not find Sohrab where he was supposed to be: the director of the orphanage tells them that a Taliban official comes often, brings cash and usually takes a girl back with him. Once in a while however, he takes a boy, recently Sohrab. The director tells Amir to go to a soccer match and the man "who does the speeches" is the man who took Sohrab. Farid manages to secure an appointment with the speaker at his home, by saying that he and Amir have "personal business" with him.
At the house, Amir has his meeting with the man in sunglasses,who says the man who does the speeches is not available,. The man in sunglasses is eventually revealed to be his childhood nemesis, Assef. Assef is aware of Amir's identity from the very beginning, but Amir doesn't realize who he's sitting across from until Assef starts asking about Ali, Baba and Hassan. Sohrab is being kept at the home where he is made to dance dressed in women's clothes, and it seems Assef might have been sexually assaulting him. (Sohrab later says, "I'm so dirty and full of sin. The bad man and the other two did things to me.") Assef agrees to relinquish him, but only for a price - cruelly beating Amir. However, Amir is saved when Sohrab uses his slingshot to shoot out Assef's left eye, fulfilling the threat his father had made many years before.
Amir tells Sohrab of his plans to take him back to America and possibly adopt him, and promises that he will never be sent to an orphanage again. After almost having to break that promise (after decades of war, paperwork documenting Sohrab's orphan status, as demanded by the US authorities, is impossible to get) and Sohrab attempting suicide, Amir manages to take him back to the United States and introduces him to his wife. However, Sohrab is emotionally damaged and refuses to speak or even glance at Soraya. This continues until his frozen emotions are thawed when Amir reminisces about his father, Hassan, while kite flying. Amir shows off some of Hassan’s tricks, and Sohrab begins to interact with Amir again. In the end Sohrab only shows a lopsided smile, but Amir takes to it with all his heart as he runs the kite for Sohrab, saying, "For you, a thousand times over.".