In the crossover fanfic CSI Death By Chocolate, adult Violet Beauregard, last seen post-blueberried at age 12(ish), has blue hair. And skin.
Pagally of Winter War has light purple hair, odd but hardly out of the question considering the source material. Subverting the usual implications of this trope in a fanfic, Pagally is originally presented as a more or less generic low-ranked female Arrancar, and while she plays a role as the plot goes on (and joins the shinigami side because she's more scared of Aizen than she is of them) she's not by any means one of the main protagonists of the fic.
Anthropology: When Lyra is turned into a human, her hair is the same color as her mane: mint green.
A Growing Affection: Yukihana has cyan (light blue) hair. Ayameko has gradient colored hair (blue on one side changing slowly to purple). The Kouin sisters have blue hair, but one of them changes it to green.
Some of the SUEs in Perfection Is Overrated have unnatural hair colors, such as Mariko (blue), Toki (silver) and Sekai (green), and others have unnatural colors for Japan, such as Shizune (blonde), Bachiko (blonde) and Meiko (redhead). In a deleted scene, Midori suggests looking for anyone with unusual hair colors as a possible SUE suspect, but retracts that when she realizes the mix of hair colors among the Mai Hime cast, as noted in the anime page.
In Marks of Time, some residents of Fort Collins have blue or pink hair, because in the future, hair dye is permanent until a "special shampoo" washes off the dye.
Return To Hinamizawa runs under the assumption that the unusual colours in the source material are natural, and they follow similar inheritance patterns to real hair colours.
Nightfall: The Shinobi have hair that usually matches their color scheme, Cristyle has light blue hair to match her blue armor and Hades has pink hair to match his red armor, conversely Syljaʻs hair is blonde to match her green armor.