Fate
One of the foremost themes of the novel is fate, and what, if anything, can be done to influence it. There are prophecies and predictions throughout, some of which are furthered by oaths (like how the suitors' oaths to defend Helen's husband bring the Greeks to the fated Trojan War), and others of which transcend or break oaths (eg, Achilles and Patroclus can't keep their promise to be both famous and happy). The knowledge of fate can in some ways be useful: by not killing Hector, Achilles extends his life with Patroclus by 10 years. Prophecy can allow the fated to avoid their destiny, at times to their temporary benefit, but fate is shown ultimately to conquer all, regardless of intentions.
Masculinity
The novel explores the theme of masculinity, particularly in its treatment of "women's work" and homosexual relationships. The most obvious example is Achilles being disguised as a woman, working and dancing so competently among the unmarried women that no one on Scryos except Deidameia knows his sexual identity. Achilles doesn't mind the dancing, but he doesn't like skirts limiting his motion; while other men imply that it would be shameful for others to know Achilles dressed as a woman, criticism like that doesn't bother Aristos Achaion. When Patroclus's body is burned, Achilles is the one to gather his ashes, even though that is traditionally done by women (his own ashes will be gathered by female slaves). Patroclus fills some "non-masculine" roles himself, teaching the war-prize women Greek, gathering plants with Briseis, and patiently waiting for Achilles to return from war.
Achilles and Patroclus have a both romantic and sexual relationship, which Odysseus indicates is unusual, stating that sharing a bedroll is fine enough for boys but might cause gossip among the men. Achilles has no sense of shame about his gay relationship with Patroclus, though Neoptolemus does. "Masculinity" in The Song of Achilles seems to be as complex a matter of presentation and self-confidence for the Greeks as it can be for the contemporary reader.
Pride
Pride is pivotal to the characters of The Song of Achilles, be they Greek, Trojan, or gods. Agamemnon is intensely prideful, and he becomes even more intolerably controlling when that pride is threatened. From the first time Achilles refuses to kneel to him, Agamemnon dislikes the Aristos Achaion, which culminates in the death of so many Greek soldiers. On the other side of that coin, Achilles' pride prevents him from fighting because Agamemnon won't personally apologize for disrespecting him. If it weren't for the pride of kings, it is likely that many men on both sides of the conflict would be alive.
The theme of pride is most clearly explored in moments when men supplicate themselves, throwing away their pride. Patroclus supplicates himself before Peleus so he can follow Achilles, and King Priam is a suppliant before Achilles, begging for his son's mangled body to be returned for funeral rights. Because pride is important to their cultures, supplication is intensely powerful and personal.
Honor or Greatness
A principal question asked in the novel is what makes a person honorable. Odysseus jokes that if society were organized differently, he might be Aristos Achaion instead of Achilles, if cunning were prioritized over strength. While Patroclus isn't in favor of Odysseus in general, his narration from beyond the grave seems to agree that the conflation of "skilled in combat" and "honorable" is detrimental to both individuals and society. Patroclus labors to free Achilles from the burden of remembering those he's killed, and when he considers the question Chiron poses (how do we know who is right to kill, even between a stranger and a brother?) he comes to the conclusion that no matter who you kill, you are making the wrong choice. Neoptolemus, while great by Greek standards, is proven not to be honorable or even very great in the long run. The question of honor—not only who has it, but what honor is—is one of the main themes of the text.
The Ethics of War
The novel poses a question of where the line of ethical decision-making can be drawn in war, and if it can be drawn at all. Combat and strength are shown to be mandatory parts of Greek culture, yet with Patroclus as a narrator, there is a sense that this emphasis is misplaced or even wrong. As Chiron trains Achilles and Patroclus, he encourages both of them (particularly Achilles) to consider when it is right to kill another man, and how one knows which life is more important than the other. By the end of the novel, Patroclus decides that there is no answer; whether you choose to kill your brother or a stranger, you are wrong. This is easier for Patroclus to say than Achilles, because Achilles is fated to be a killer, regardless of ethics. Chiron's other questions (including "How will you respond when men ask you to fight their battles?") encourage both the characters and the reader to confront the moral puzzle of warfare and its necessity.
Legacy
The Song of Achilles is a text obsessed with legacy, as we watch Patroclus and Achilles influence and confront what will happen to them after death. Achilles is promised fame, a legacy to last the ages, but still he worries about how famous he is prophesied to be in exchange for his short, bright life. Patroclus sublimates his own desire for conflict-avoidance in order to become a sort of record-keeper for Achilles, imagining himself making an "urn" (some of the most long-lasting relics of ancient Greece) out of Achilles' violence. Odysseus jokes that perhaps his cleverness will eventually lead to an even greater legacy than the most efficient of soldiers. Each of the characters must think of his legacy before he considers his day-to-day actions. More broadly, The Song of Achilles itself is continuing the legacies of these men (if they truly lived); the fact of the novel invites questions of how we tell Patroclus's story, and why, and who tells it, with what agenda.
Love
The Song of Achilles is at its heart a tale of love that transcends death. Achilles and Patroclus develop a romance that conquers immortal disapproval, multiple disappearances, a pregnancy, and a decade-long war. Their homosexual relationship is unusual among adult Greek men. Neoptolemus wants all memory of it removed from his father's legacy, but their romance constitutes a majority of the novel—Neoptolemus's desires are directly flaunted by the fact we are discussing Patroclus some two millennia after he is said to have lived.
Other forms of love are present in the novel as well, though they are secondary to the romantic core. The only examples of wholesome family love come from Priam, King of Troy, and his son Hector. Odysseus loves his wife and son, to be sure, but Patroclus doubts Odysseus even has a wife for most of the novel. Other Greeks are shown to be too consumed by honor or legacy to worry much about love. Patroclus develops a lasting platonic love for Briseis; Thetis adores Achilles in a way that preempts her acceptance of his mortal ability to love. Patroclus's love for nature and, broadly, all living things, makes him a compelling narrator—one very different from the usual grand Homeric hero.