Ayaka Shiramine has everything going for her: a beautiful, kind, and hard-working girl, she is the star of Seiran Academy—at least, that was the case before she moved up to the academy's high school division. Enter Yurine Kurosawa, an aloof and friendless girl who excels at everything from academics to housework without lifting a finger. In fact, she seems to surpass Ayaka in almost all aspects, and the former star student quickly begins to despise her new rival.

Despite her disdain for Yurine, Ayaka's kind nature and a push in the right direction help Yurine to begin making friends... and fall head-over-heels for the girl who hates her. Meanwhile, Ayaka struggles to deal with her growing feelings towards Yurine; though she can't stand the girl who knocked her down to number two, she finds herself falling in love with her.

Ano Ko ni Kiss to Shirayuri wo tells the story of two seemingly perfect girls who, while still searching for their place in the world, have at least found someone in a similar dilemma: each other.