Because its themes of friendship, betrayal, guilt, redemption and the uneasy love between fathers and sons are universal themes, and not specifically Afghan, the book has been able to reach across cultural, racial, religious and gender gaps to resonate with readers of varying backgrounds.

— Khaled Hosseini, 2005[3]

The whole story’s theme revolves around this piece of advice given by Baba to Amir,“When you kill a man, you steal a life,” Baba said. “You steal his wife’s right to a husband, rob his children of a father. When you tell a lie, you steal someone’s right to the truth. When you cheat, you steal the right to fairness.”In one way or another, all the characters involved have committed these offending crimes. Questioning to what extent Baba himself was able to keep up with his advice, to question whether he was harsh on Amir just because he hated himself for what he did, and ultimately the story ends with poor Hassan being the victim, Baba dying of guilt and an unresolved problem that Amir later discovers to pay the price and make things right again.

Khaled Hosseini identifies a number of themes that appear in The Kite Runner, but reviewers have focused on guilt and redemption.[9][11][19] As a child, Amir fails to save Hassan in an act of cowardice and afterwards suffers from an all-consuming guilt. Even after leaving the country, moving to America, marrying, and becoming a successful writer, he is unable to forget the incident. Hassan is "the all-sacrificing Christ-figure, the one who, even in death, calls Amir to redemption".[19] Following Hassan's death at the hands of the Taliban, Amir begins to redeem himself through the rescue of Hassan's son, Sohrab.[20] Hosseini draws parallels during the search for Sohrab to create an impression of poetic justice; for example, Amir sustains a split lip after being severely beaten, similar to Hassan's harelip.[20] Despite this, some critics questioned whether the protagonist had fully redeemed himself.[21]

Amir's motivation for the childhood betrayal is rooted in his insecurities regarding his relationship with his father.[22] The relationship between parents and their children features prominently in the novel, and in an interview, Hosseini elaborated:

Both [The Kite Runner and A Thousand Splendid Suns] are multigenerational, and so the relationship between parent and child, with all of its manifest complexities and contradictions, is a prominent theme. I did not intend this, but I am keenly interested, it appears, in the way parents and children love, disappoint, and in the end honor each other. In one way, the two novels are corollaries: The Kite Runner was a father-son story, and A Thousand Splendid Suns can be seen as a mother-daughter story.[2]

When adapting The Kite Runner for the theatre, Director Eric Rose stated that he was drawn into the narrative by the "themes of betraying your best friend for the love of your father", which he compared to Shakespearean literature.[23] Throughout the story, Amir craves his father's affection;[22] his father, in turn, loves Amir but favors Hassan,[20] going as far as to pay for plastic surgery to repair the latter's cleft lip.[24]