Mycena nidificata was first collected in 2000 by Japanese mycologist Haruki Takahashi, and reported as new along with seven other Mycenas in a 2007 publication.
According to Takahashi, the inamyloid spores, the diverticulate cap cuticle hyphae, and the dark pigment in the gill hyphae suggest that the fungus is best classified in the section Hiemales of the genus Mycena.