Flaveria vaginata is a very rare Mexican plant species of yellowtops within the sunflower family. It has been found only in two locations in central Mexico, one in northwestern Oaxaca, the other in southwestern Puebla.

Flaveria vaginata is distinguished from related species in the genus by its dense woolly pubescence on the upper leaves, and by the fact that the flower heads are concentrated into dense hemispherical clumps.