Australian mycologists Melissa Danks, Teresa Lebel and Karl Vernes first described the species in the journal Persoonia in 2010. The type collection was made near Mount Kaputar, in New South Wales (Australia) in July 2007. Although some of the characteristics of the fruit body (such as the pigmented cap and veil) suggest a placement in the section Dermocybe of Cortinarius, molecular analysis of internal transcribed spacer DNA sequences indicates affinity with species in the section Phlegmacium, along with the Australian species C. austrovaginatus and C. sinapicolor. The specific epithet kaputarensis refers to the type locality.