The narrator's epiphany—the sudden awareness or feeling of knowledge of something new—arrives at the end of the story, when she realizes that she cannot "protest" her father's statement that "She's only a girl," because "Maybe it was true." Prior to this, she had enjoyed working alongside her father and even hid, with her brother Laird, to watch while her father and his farmhand shot a horse between the eyes.
Although the sight was not something she ever wanted to witness again, Laird was eager to go with the men, some months later, to capture and kill another horse that had escaped. The narrator had had an opportunity to stop that other horse, but, instead, she opened the gate wide so the horse could run away. When the men come home with the dead and butchered horse, she cries while her brother is matter-of-fact. It becomes clear to her at this point that there is some fundamental difference between herself and her father and brother.
The narrator's father also seems to have an epiphany, once Laird reveals to everyone that the narrator purposely let the horse escape. He speaks with "resignation, even good humor" when he explains away her behavior with the words that both "absolved and dismissed" her forever: "She's only a girl." He knows, now, that she has reached an age at which her interests and feelings begin to change—and we know this to be true because of what she, herself, tells us. He is resigned to her growing up, though perhaps a little saddened by it.
The epiphany experienced by the narrator of Alice Munro's "Boys and Girls" occurs when she realizes that her father, who has been her principal role model and mentor, will never see her in the same way that he sees his son and that something essential and inevitable separates her from the male members of her family. Throughout the story, she has felt far more at home in her father's domain, the fox farm, which is orderly and dynamic, than inside the house, a place she associates with her mother and by extension with femininity. She has always tended to dismiss everything she regards as feminine.
When the narrator, who significantly, unlike her brother, is not named, opens the gate to let out Flora (for even the horse has a name), her father dismisses this act as typically feminine. The narrator realizes at this point that she cannot simply follow in her father's footsteps, as her brother can, but will have to work out life for herself, including gender relationships and what it means to be a girl and eventually a woman.
One could argue that the epiphany in the story takes place when the girl realizes that she's a girl after all, not a boy. Up until that moment, the narrator had always been an incorrigible tomboy, accompanying her father everywhere on the farm and doing the same kind of things that boys normally do. For good measure, she always dreaded the idea of being moulded into a fine, respectable lady by her mother, whose notions of gender roles are thoroughly traditional.
And yet the girl gets in touch with her femininity when she tries to save the old nag Flora from being shot. In this moment of epiphany, it's as if the girl has internalized the ideal of femininity constantly drummed into her by her mother and grandmother and has finally come to realize that participating in the bloody day-to-business of working on a farm is unsuitable for a lady.
An epiphany is a sudden realization, usually by a character, that provides insight into an important situation and often inspires that character to change course. In Alice Munro’s story, one important epiphany occurs when the unnamed female protagonist realizes that her brother is becoming more like her father, and they both will never fully accept her because she is female. This epiphany occurs in conjunction with the girl’s decision to open the gate and let out Flora, the horse. This action, which her father quickly dismisses as gender-related, prompts her to consider the more enduring consequences. The girl sees that she must live her life according to her own principles: she must decide for herself what it means to be “only a girl.” The choices she makes will inevitably involve disagreements with her father and mother, especially concerning appropriate gender roles.